To be fair most chemistry students experimenting with explosive materials never intend to blow anything up.

I can understand why they might have thought he was operating a meth lab, aside from the lack of output of meth, or any connection to meth dealers, or was in fact being bankrolled by a local meth corporation or anything like that.

What I can't understand is then taking the view that he has to be imprisoned anyway, and trying to stick him with a charge that requires intent, and thus isn't exactly hard to get out of.

As forms of petty police harassment go, it's a very expensive and pointless one.