The Tesla boss took to social media to reveal the problems but did not elaborate on what they actually were. Musk did say that future missions will "definitely" include "upgraded toilets" to make sure they don't happen again.
Musk had met with the crew after they touched down in Florida where he was informed of the problems, even though the discussion pre-flight centred on how good the facilities were.
They were located just beneath the 'cupola', a huge built-in window, allowing the crew to look out into space as they relieved themselves.
Jared Isaacman, the billionaire who funded the trip, added that the toilet was covered by a curtain to offer some privacy for those on board.
SpaceX hasn't disclosed much about how the toilet works but training on it was part of the preparation regime that the four-strong crew had to go through prior to the flight.
Musk also intends to add other improvements for future voyages, including a "little oven for heating food" after the passengers were forced to eat cold pizza.
The tech guru added that the ship will include a WiFi connection through SpaceX's Starlink satellites.
The SpaceX venture concluded on Saturday (18.09.21) and Musk welcomed the crew home with a $50 million donation to the children's charity St Jude, as the passengers were aiming to raise $200 million for the St Jude's Children's Research Hospital in Tennessee.