Everyone's eyes are going to be different, so matter what kind of eye was transplanted, the patient's brain would no doubt have to spend some time getting accustomed to it (assuming that vision was restored, which hasn't been done yet in humans). However, growing the nerves necessary to restore vision would also take time, so they probably would not notice color in particular being confusing. Everything would be confusing while the nerves regrow.
After vision was fully restored, they presumably would just have reduced color vision in that eye, but their other eye (if they had one) would pick up the slack. It wouldn't be that different from people who are partially blind in one eye; the brain puts together the information from both eyes and constructs a single coherent image from it, such that it's not really noticeable to them that their two eyes see differently.
After vision was fully restored, they presumably would just have reduced color vision in that eye, but their other eye (if they had one) would pick up the slack. It wouldn't be that different from people who are partially blind in one eye; the brain puts together the information from both eyes and constructs a single coherent image from it, such that it's not really noticeable to them that their two eyes see differently.