I don't know if your hopper was like that when you received it, but this appears to be another flaw. My "hopper" is tight when the unit is cold, but is easily tipped side-to side when the unit heats up. It's possible (and the photos seem to indicate) that it is simply melting, and when any movement of the hopper occurs while the pipe is hot, it's deforming the fit.
One of the first things I did was to cut a couple of pieces of material to hold the "hopper" in position, as the enclosure has a large, oversize hole, which does not do this. So far, so good.
As for the waves, when starting the unit, I pull the filament out as indicate above, but it really doesn't matter if you stretch it. In fact, I usually pull it until it is very thin, and baby it a bit until it follows the guides. Some have used a wooden clothespin on the end to make sure there is enough weight to keep it taut until there is enough filament to do that on it's own.