I have an iPad 3 and use Infuse and VLC to play videos on my iPad. Now I am having a weird issue. I am trying to play a TV series that a friend gave to me. The files are mkv. The resolution is 1280x718, which is surprising, as file size is only 90 MB for a 25 min video. Now when I play these videos on my iPad, the video sort of freezes every second. They play fine on my PC. I tried using both infuse and vlc but same issue. I think the files must be compressed in some way, as I have seen that 25 min of a 1280x720 video can be upto 400 MB in size, I have played such videos on my iPad, and they play fine.
Your suspicions on a 90mb file not being HD are correct. A 25 minute show that is HD would not be 90mb. Hell, that's even small for standard definition quality. Resolution and file size are very different. You can have a video file that is super compressed, but still runs in a higher resolution. The end-result will be a wide & tall, but blurry, picture quality.
As for why they are freezing on your iPad, it's possible that the conversion settings were a little off when someone created this file. I think this based on the small file size, mixed with high resolutions. It sounds like someone was trying very had to make a small file size and probably tweaked a bunch of settings on the export file to do so. It's possible the software you are trying to render it with (VLC, Infuse) are struggling to interpret the file. As you mentioned, the iPad can play other files fine.