Question: I just realized that both seems to mean the same thing. However, I am not sure if this is something that's context-dependent or not. What do you think?

For example:

> 
> I pressed and used the buttons at the right time and in the right
>  combination.
> 
> 
> I pressed and used the buttons at the right time and with the right
>  combination.
> 
> 
>

Answer: 
Interesting question! I've never thought about this before.

This might depend on the individual and the dialect, so I will only be answering for myself and Australian English.

**In** a combination is used to describe a series of actions (for example, pressing buttons) being done in a particular order. The actions themselves are the combination.

> 
> I pressed the buttons in the right combination.
> 
> 
> 

**With** a combination is used to describe an action (for example, opening a lock) that needs to *use* a combination (a particular sequence). The action is not part of the combination.

> 
> I opened the lock with the right combination.
> 
> 
> 

So in your question, **"in the right combination" is correct.**
I suggest using *I pressed and used the buttons in combination with right time and right combination*. If you'd like to use *with the right combination* I think you should add *of sth* after combination, i.e. *with the right combination of sth* Please refer to [this post](https://english.stackexchange.com/questions/76954/difference-between-combination-of-and-combination-between)