Mata was voted as Chelsea's player of the year for the last two seasons but found himself out of favour under Mourinho, who opted to build his team around Oscar instead.
"I feel sorry that I didn't make him happy, but football is football and I build a team around Oscar in that position and on the sides the other people is doing very, very well," Mourinho told reporters.
"Juan is not comfortable on the sides. He tried very hard and he did very well in some matches playing on the sides, but it's not his natural habitat.
"So when a club like Man United comes and for sure they told him he's going to play in his favourite position and he wants to go, he goes."