Why don't Marvel movies stick to canon?

Why don't they get script writers to stick to the comic book facts?

And what comic book facts are these, exactly?

Marvel have repeatedly ret-conned and rebooted the majority of their characters at some point in the past: even within the same Universe its almost impossible to find a character with a totally non-contradictory history.

There have been over 30 different versions of Spider-Man,for example: and even recently, many of these are published concurrently: Superior Spider-Man, Ultimate Spider-Man and Amazing Spider-Man are all supposed to be the 'Same' individual, but there are still off-shoots like Scarlet Spider...

In order to address these discrepancies, Mark Gruenwald created a 'Universe Designation' cataloging system in his fanzine 'Omnibus', which has since been adopted by the comics themselves. There are now several alternate realities of Marvel operating side by side: The Main comics universe is Earth 616, the Ultimates Universe is Earth-1610 and the MCU universe is Earth-199999.

There are no clear, consistent 'comic book facts' in Marvel Lore; it is constantly being renegotiated by different writers who will change details of individual narratives to serve Retcons, Reboots, or Remediation.

The MCU is an example of property remediation: Marvel are adapting their recognisable and well circulated comic book stories into film, and as such will change them to suit the new medium (and to create something new, instead of just retreading the same old familiar).

There are no comic book facts, and MCU writers are electing to do just that: to write Something new, something different, something less predictable but still familiar.

It's important to realize that the Movies aren't even supposed to be set in the same universe as the comics: they use referential paratexts to the comics, like Easter eggs; but they're within a separate continuity.

First things first, Marvel rights are split between Disney (main owner), Fox, and Sony. So the reason for changes depends on the owner of the rights.

For the case of Iron-man, Disney has all the rights of the comics and movies of Iron-man. They are free to do anything with the character. There are many Iron-Man comics now. If they stick with the plot of the comics, then they would have to make many movies to cover it. Extremis' arc is also far too long to adapt into a single movie, so they decided to go with the fusion of plots (and it worked).

For the case of X-men, the rights are with Fox. X-men movies were already ruined with respect to continuity, so Fox tried to reunite with Days of Future Past. So if you want them to stick to the comics, then they can't include the cast from First Class because the story from First Class wasn't in the comics. Kitty Pryde is not used to traveling to the past because she wasn't there in First Class and she was quite young in X-Men 3. So she can't be used as a mind-time-traveler. So her skills were modified to make Wolverine the traveler.