Sean, try and wiggle the frames a little as you put them back or before putting the frames in place watch carefully, as you place the frame and see if there are any bees between the edge of the frame and your hive box. If there are give them a second before you lower the frame completely. Now if you are pushing frames together, you need to do it gently. Give the bees a little time to move out of your way as you are moving the frames back in place. You will get better at it with time. Same thing with the top cover, slightly wiggle, slightly lower at the same time, give them a second to get outta the way. It will also help when putting on the cover to smoke them a little as well, if they are piled on top, this will cause them to move down and out of the way. Good luck, hope this helps.