The thing with Stain is that Iida sought him out. In fact, all of the student came to the scene of their own accord, effectively looking for trouble. If Stain had attacked Manual, Or Iida was interning with Native when he was attacked, Iida at least would be completely in the clear. They could have even spun a tale like "I gave Iida permission to engage to save his life, and when Midoriya found him and tried and failed to get Iida out of here, I gave that kid permission to engage, too because I'm not gonna let him get cut up. And then that third kid showed up, and I gave him permission to fight because if I'm already handing out permission..."
Also it was more about the fact that what they did was technically vigilantism, they were student of the most popular hero training school in Japan, which they couldn't deny because they came in Top 8, 3rd place, and Runner-up of the sports festival that was broadcast all over Japan and potentially worldwide.