Why do turtles that have been alone for a long time not like company?

What kind of company? Turtles are not aggressive and will tolerate the company of humans other animals and, depending on the species, other turtles fairly well. But they are not social animals. They don't crave friends and contact. They like to have other turtles to mate with during mating season but neither the mother nor the father has anything to do with the babies. They are on their own. Turtles are territorial and males will sometimes not tolerate the presence of other males. If you spent a lot of time with your turtle and then left it alone for a long time it is possible that it's tolerance for being played with has somewhat gone away. But, if you spend more time with your turtle it will most likely get used to that again. Hope this helps!