Ok, I made this mistake at Disney. One night I thought I would be smart and I put the water bottle in the freezer with the filter inplace so all I had to do the next morning was grab and go. Well, the filter had ice on it and water wasn't coming out. When I pulled the filter out it was a frozen mess. Note to self: do not freeze filter. OK, so the next night remembering what a mess the filter was (it may have been fine after it thawed...I never bothered to check) I put the bottles in the freezer without the filter. The freezers in the little fridges at Disney are not big enough for the bottles to stand, so they had to lay down. Well, now the water is along the side from end to end (top to bottom). In the morning when go to put the filter in, I couldn't because ice was blocking part of the hole. I had to thaw it out a bit and get the ice away from the opening. I found that just some ice and water worked really well and was really easy.
Now, when I'm at home, I have put the bottles in the freezer, upright and without the filter. I haven't had a problem doing it this way.