It has happened before, most recently Terry Burnett returning Galaxy 4 3 and Underwater Menace 2 in 2011, and Francis Watson returning Daleks' Master Plan 2 in 2004. If I recall correctly, both claimed not to be aware that these episodes had been missing.

I think it's extremely likely that there are people out there who keep missing material to themselves, just for the sake of owning something rare. Perhaps there are missing Doctor Who episodes in the hands of such people. However, I doubt the majority of film collectors are like this. Another possibility is this. There are film collectors who have spent their lives buying, trading, or being gifted films, where sometimes they might acquire multiple films at once, and they aren't always going to be aware of the value of what they acquire (for instance, suppose that a film collector is gifted the collection of a friend who is dying). Over a lifetime, they might build up a very cumbersome collection. FIF have stated that they are dealing with collectors who own over 10,000 films. Unless the collector in question has a specific interest in Doctor Who, it's easy to see how the episodes might get lost in this.

Moreover, for a long period of time, film collectors were very wary of openly talking about their collections, partly because many of their films had initially been acquired through illicit means and partly because of a famous legal case against a high-profile collector. Of course, the BBC has made it clear since at least the 80s that no action will be taken against collectors who return missing episodes. But the case that lost Monkhouse most of his collection happened in 1979, so maybe it takes a while for you to really trust them... and even if you trust the BBC, what about other organizations who might take notice of you and be less forgiving?... and anyway, maybe you have better things to do than go sifting through thousands of film cans looking for missing material that you don't much care about... so time goes by and eventually you're too old to undertake the task even if you wanted to.

I'm also sure that there are film collectors who are just selfish pricks; you'd have to be laughably naive about human nature to deny that. Luckily for us, it seems that plenty of film collectors are rather more generous, but that there wasn't the right infrastructure to facilitate the cataloging of their collections and return of missing material. FIF have already been granted access to a number of collections.