The game saves and loads at various times. If you have the game running in place A while playing (and thus saving) in place B, and then continue playing in place A, the next save will likely overwrite everything you did in place B.
Simplest way to avoid this would be to reload the page (so you'll have to login again) before starting to play, if you've left the game running while playing somewhere else, as that way you'll force a load, kind of.
As for the stop playing bit, it saves time I guess. If you're talking pvp, it might just be that they lost connection or desynched.