What happen at the end of the third Madoka Magica movie? I just watched the third movie (Puella Magi Madoka Magica the Movie Part 3: Rebellion) and I have a doubt about the fact that although Madoka wish in the second movie, which prevented the birth of any witch, both in the past and in the future. Why then Homura becomes a Witch?

I get an idea, but I'm not pretty sure about it. In the ending we see Homura feeding QB with her soul gem. Does this mean that all the curses of the universe are now contained in Homura's soul gem? And that feeding QB with them is a way to stop entropy?

When Homura says to Sayaka and Madoka that one day they will be enemies, is she referring to the fact that without suffering sooner or later the universe will run out of energy and Madoka and Sayaka will have to stop her?
Ok, let me try to answer this the best I can. I've watched the movie twice: in a theatre in Paris and the subbed camrip that's been going around.

although Madoka wish in the second movie, which prevented the birth of any witch, both in the past and in the future. Why then Homura becomes a Witch?

Madoka's wish wasn't exactly that. She wished to erase all the witches, past, present and future with her own hands. The bolded part being the interesting one. Not only did it mean the wish couldn't have any unfortunate fulfilling that wasn't what she wanted, it meant she would have to do the work herself. Which is also the only reason it invokes a paradox that forces her existence into a concept. Either way, the point is, Madoka takes the despair out of the Soul Gems of Magical Girls as they are about to become witches. The natural tainting process of the Soul Gem still exists and the girls would still become witches if she wasn't there to take their souls to wherever and let them have a dignified death.
Only in Homura's case this time, she wasn't there. To expand upon it, what the Incubators do is use their super advanced alien science to freeze Homura's Soul Gem at a borderline state. She's about to become a witch, but she's still a magical girl. Let's say for the sake of an analogy that her Soul Gem was 99.99% tainted. That's where they froze her at. Because that's the point at which Madoka would come in and save her from becoming a witch as she did to everyone throughout the series and they wanted to capture Madoka. So, frozen at this state, the Soul Gem couldn't break and impose a witch barrier over some part of this world (which is still a separate dimension of its own), so it created a barrier of sorts inside itself. Basically, the first part of the movie was spent inside Homura's Soul Gem. Note that at this point, the world they're in may be akin to a witch barrier, but Homura isn't a witch, as the barrier was created by what is still her Soul Gem.
After the whole ordeal that culminates with her realizing she's the one who created the barrier, Homura is confronted by Kyubey, who tells her about what exactly had happened with her and what their plans for Madoka were. There, she decides to become a witch inside the barrier so she can be killed by Mami and Kyouko there and ensuring Madoka will never come for her. Note that this Homura inside the Soul Gem is basically her soul, so being killed inside it is the same as destroying her Soul Gem. Now she purposely brings upon her more despair and suffering by accepting she won't be able to meet Madoka again and successfully becomes a witch inside the Soul Gem. This is a separate world of its own, one that Madoka can't see nor reach (which is still kinda of a moot point anyway since Madoka is trapped inside it without any memories of who she even is), which is why it was possible for that to happen. The Homura in the outside world, her physical body, is not yet a witch, since any developments in the inside won't affect the outside thanks to Kyubey's filter.
TL;DR - Homura doesn't become a witch in the outside world, she becomes one inside her own Soul Gem, which is a separate dimension from the one Madoka can see and interact with.

I get an idea, but I'm not pretty sure about it. In the ending we see Homura feeding QB with her soul gem.

We do? I'm pretty sure that's not what happens so... By ending, are you referring to the post-ending credits? Since that's the only thing I think could have been mistaken by that. But we never see that. All we see is Kyubey appearing, Homura bringing up her Soul Gem, perspective change, her legs doing some sort of dance, perspective change, her dancing with a beaten-up Kyubey in the background. If what you're saying does happen at any point, please specify.

When Homura says to Sayaka and Madoka that one day they will be enemies, is she referring to the fact that without suffering sooner or later the universe will run out of energy and Madoka and Sayaka will have to stop her?

That point is pretty much up in the air, specially her words toward Sayaka. What she says to Madoka is easier to interpret, though. She asks her about her ideals, if she thinks the world is more important than the happiness of one people. Basically "selflessness vs selfishness". And Madoka answers with the former. What this conversation shows is that Homura is fully aware her actions were selfish ones, but won't back down on them since it's what she's always wished for. Madoka's answer, though, goes against the very thing she won't back down from, which means their ideals at the moment are complete opposites, so if Madoka ever understands the situation and comes to want to realize her ideal, it'd only be natural they would become enemies. Which will eventually happen, since it's very doubtful Homura will be able to keep the world as is without either Madoka or Sayaka getting at least part of their memories back. Heck, things were already turning out that way with Madoka and would have if Homura didn't hug her into submission.

Before proceeding, please have in mind that while everything before this paragraph are things I'm nearly certain of having interpreted correctly, this isn't but a theory of mine:

Back to the Sayaka conversation, that's one of the issues I have with this movie, in that Sayaka's question regarding destroying the world came out of absolute nowhere and Homura's answer made no sense at all, considering she says "Once all wraiths are defeated". And since we know from the series the wraiths are the new embodiment of grief and despair in a witch-less world, and that hope and despair can never triumph over one another since the Madoka world is a zero sum game, that makes absolutely no sense at all. So I've thought a lot about that until now and I think a possible (even if not obvious as the one for the Madoka conversation) interpretation is that Homura implying the wraiths will eventually be eliminated means she is, herself, trying to become the embodiment of despair. That way, she'd become a true counterpart to Madoka, who's the embodiment of hope, and the balance would be restored.