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The first time it happened, Scott had a complete freak out. He'd had a few questions for Derek about the next full moon and had gone to the abandoned subway to get some answers. Instead he'd walked in on his best friend having (really loud, really enthusiastic) sex with his alpha. It would be enough to freak anyone out, in his opinion, especially when he'd thought the two barely tolerated each other most of the time.
He'd gone straight to Allison, hoping for some sympathy and comfort for his scarred mind. Instead, she'd sneakily asked about the sex and he'd started answering before he realized that he really didn't want to think about it, much less talk about it. Strangely, Allison was rather disappointed that he wouldn't divulge any details.
The second time it happened, Scott freaked out a little less than the first time, but not by much. He'd just wanted to get Stiles to help him with his chemistry homework (he might be able to pass if he did all the homework really well) and he'd figured Stiles' room would be safe seeing as the sheriff lived in the house too. Of course he wasn't so lucky.
This time Allison tried to fake a bit of sympathy before pestering him for details. He decided that maybe a bit of quiet denial at his own house would be a better idea, especially when he caught a hint of arousal from his girlfriend. He didn't want to think about her being turned on by Stiles and Derek having sex and really, he was too traumatized for sex himself if that wasn't the case.
The third time it happened, Scott just rolled his eyes and decided to take a shower at home, or maybe at Allison's. Either way, he wasn't sure if he'd ever be able to go the shower section of the lacrosse locker room again without thinking about what he'd just seen.
He ended up at Allison's house under the guise of taking a shower there while his was broken, but she knew right away what the real reason was. She was more persistent in her questioning this time and he was a little less freaked out this time, so he went ahead and told her about it. This time he was sure the arousal he was smelling was due to what he was telling her. And well, he didn't think he was too traumatized for sex this time.