Document your concerns - all of them. And if you're not sure if your son is giving you completely accurate info, it is still how the experience is affecting him and therefore valid. Just couch those sentences in phrases like "he has said" "he mentioned" etc.
I dealt with similar problems one year with a teacher who was convinced that "natural consequences - which were far too often not natural but punitive and manufactured by her" would cure my son of the aspects of his disabilities she found annoying. It was a tough year.
I would point out that the consequence was punitive and ostracized him in front of his peers by insinuating that he was too immature and underdeveloped by being forced to spend the morning with children in Kindergarten. Express concern about the failure to provide adequate notification to you as the parent; whether your child has LD's or not, kids this age forget to give papers to parents - and a major project that requires work at home should have started with requiring a signed note about the scope of the project and the due dates. Then the teacher would have known well in advance that you were not aware and could reach out in time to rectify the situation.
I let my kids crash and burn when it was appropriate - when they made little or no effort on a project, when they chose to resist help being offered, etc. But this doesn't sound like one of those times.
And as awful as it has been, at least you now have a perfect example to point to when you start asking for modifications and supports.
