At my pervious airline, we had a free seating policy, and I often had problems with non ABPs (Able Bodied Passenger) trying to occupy them. particularly cause our seat pitch was so small, there were some pax who simply couldn't fit comfortably in a normal seat. The key to dealing with this problem, is being vigilant, and using a bit of tact.
I only ever ended up having a real problem once, when a particularly large and tall lady refused to sit anywhere else. Despite all my attempts at being nice, she still refused, and I ended up having to be quite assertive, which probably came across as rude. I spoke fairly loudly explaining that by law she wasn't allowed to sit there, and that if she didn't move right now, it would delay the aircraft. If we missed our slot, we would then be delayed up to a further hour, and that it wasn't very fair on the other passengers to be delayed over this kind of situation.
I'm still only fairly new to flying, so would appreciate more senior pruners giving suggestions on how i could have dealt with the situation better. I tried to be nice, but it just didn't work. I did feel quite bad about it afterwards though.