Mr Museveni, 71, is seeking to extend his 30-year rule, in a race widely seen as the tightest in the East African state's history.
His main rival Kizza Besigye was briefly detained by police.
A foreign observer group condemned the blockage of social media and lengthy delays in opening voting booths.
Uganda decides: Live updates
Uganda's election explained
Interviewed on TV about social media, Mr Museveni said: "Some people misuse those pathways. You know how they misuse them - telling lies.
"If you want a right then use it properly."
Many people found a way around the controversial restrictions, including opposition candidate Amama Mbabazi who tweeted advice on how to do it:
A VPN - a Virtual Private Network - gets round government censorship by redirecting your internet activity to a computer in a different country.
Facebook, Twitter, Whatsapp and mobile money services were blocked.
Despite this, #UgandaDecides was trending on Twitter.
Commonwealth election observer mission head Olusegun Obasanjo said: "It is ill advised if anyone has blocked social media."
Condemning the failure of voting stations to open on time, he said: "Delays of three, four, five and even six hours, especially in Kampala, are absolutely inexcusable and will not inspire trust and confidence in the system and the process".
The electoral commission said difficulties in transporting electoral materials caused the delays, and voting at some polling stations would continue on Friday.
The BBC's Catherine Byaruhanga in the capital, Kampala, reports that crowds were angry after waiting several hours to vote and police fired tear gas to disperse them.
Voting was cancelled at at least two polling stations in the city after clashes with police and accusations of fake ballots being distributed.
Some voters in Kampala, traditionally an opposition stronghold, accused the authorities of deliberately stalling the vote, AFP news agency reports.
"People are quite angry and everybody is believing that there is something  wrong behind this because of the way they are delaying things," Moses  Omony, a motorbike taxi driver, is quoted as saying.
Mr Besigye was arrested for demanding access to a house in Kampala where he believed vote rigging was taking place following the closure of polling stations, said Ssemujju Ibrahim Nganda, spokesman for his FDC party.
He was taken to a police station before being released.
Mr Besigye is among seven opposition candidates hoping to end Mr Museveni's 30-year rule.
A candidate needs to secure more than 50% of the vote to avoid a run-off with the second-ranked contender.
Ugandans also voted in parliamentary elections.
Counting is under way and official results are expected by Saturday.
Major presidential contenders:
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Social media has been blocked in Uganda on the day of presidential elections to stop people "telling lies", President Yoweri Museveni has said.