Yea. If the person transforms into an inanimate object(rock, tree, etc) the sharingan will be able to see there's chakra in those objects and know #BS is occuring.
If they transform into someone else, the sharingan user can tell that person is a fake if they know their targets chakra. Like, If naruto transforms into sakura, kakashi can most likely tell it's not the real sakura. This part is based on the fact that people like shishui had special colour to their chakra so i'm assuming everyone's chakra is slightly different..