Cover of "Contact"
Cover of Contact
The most scientifically accurate science fiction film has to be "Contact". It gives perhaps the most plausible and accurate depiction of how mankind may actually come in contact with an alien species. It is written by Carl Sagan (celebrated astrophysicist) and that explains the scientific accuracy. It does away with all the alien invasion and battle for survival of race crap but still gives you an engaging storyline. I strongly suggest you watch it .

It is usually the action and thrill quotient which takes the movies in implausible domain. All the superhero movies and Pacific Rim et al start with impossible premises because they try to be grandeur filled action adventure feasts and hence require ridiculous things to happen.
My favorite kind of science fiction is one which is based on a revolutionary concept or idea and the storyline develops the idea further rather than just milking it to create CGI filled action sequences.
Some others that come to mind are - 

1. Looper (the Telekinesis bit is disputable though)
2. I-Robot (except it becomes an action fest in the end).

Of course none of these come even remotely close to Contact in terms of scientific accuracy.