I’m assuming these are .SMD since .MGD aren’t accepted by the emulator.
This could occur if the file’s size wasn’t an increment of 16kB. The SMD file format breaks the file in to blocks of 16k then swaps bits around so that all the even bits are at the beginning of the block and odd bits at the end. So I read the file in chunks of 16k assuming it is possible since all no-intro entries except a couple prototypes have sizes divisible by 16384.
The other possibility is there is a bug. I’ll read over the code and write some tests. In the meantime, do you mind checking the size of a couple of these to confirm they are indeed divisible by 16384.