I think it's your ignition coil. On most 1-speed Puchs, the ignition coil attaches to the front of the engine, on the right side to a bolt just behind the cylinder. Your side covers are for that configuration, so your ignition coil is blocking them from sitting correctly.
The original side covers for bikes like yours have a cut-out for the ignition coil to stick through. So, you could either cut a hole for it, get different side covers, or see if you can attach the ignition coil to the front of the engine.
Did your bike used to have a 2-speed engine?