Pencil is messing up my animations! It continues to take a frame on a layer and move it somewhere else, or even make it disappear completely! It is also going so slow I can’t fix anything. It’s things like this that keep pencil from being great.
“take a frame on a layer and move it somewhere else”
I think you should click on a layer first before you select a frame on that layer to move it.
“or even make it disappear completely!”
I don’t know how this happen. You should elaborate your problems more please. Thank you. 
Keep in mind that even though Pencil has been developing for a long time, Pencil’s development is very slow. It feels like it’s still a new program (like it’s a 6 months old program) and someone needs to improve it. Matt hadn’t got the time to develop last year. So hopefully he (and other people who want to help) have the time to develop
Also, I assume that you’re using 0.5 now. You need to know that 0.5 is still less stable. I suggest you to use 0.4.4b if you can’t handle 0.5.