The Spaniard reportedly had a disagreement with the Frenchman following the Toffees' 3-0 defeat to Swansea City in the Capital One Cup last month.
After that game, Distin did not feature for two weeks, but Martinez has insisted that a minor injury forced the defender out of the team.
"You will always get rumours, but the reality was that he picked up a knock after the Swansea game and obviously at that period I considered it was right for him to have a bit of break and rejuvenate," Martinez told reporters.
"But sometimes he is such a professional he works too hard. He is someone who is not just happy with what he does with the team, he has his individual programmes and he works too much.
"I felt that he needed a bit of a break but now he has come back refreshed and ready to fight for his place. Sylvain is training well and is fully refreshed and is ready to fight for his place."