There's a problem playing movies in BD ISOs which use seamless branching. When the branch should occur, the Mini 2 will sometimes pause for a second or two and then play correctly, more often than that (and more seriously) it will stop completely and all you can do is stop the movie, or it will jump to completely the wrong part of the movie, picking the new point apparently at random.

Here's a couple of examples:-

'Paul' - this disk includes both "director's" and "normal" cuts of the movie, and uses seamless branching to insert the additional scenes. Quite early on there's an extra scene at the comic convention, but whether playing the normal or DC version, when the Mini 2 gets to that point it skips about 10 minutes further into the film.

Battle: Los Angeles - The Mini 2 constantly flicks forward through the movie, the first half an hour of the movie plays in about 10 minutes on the Mini 2.

.......

I only rip my own BDs, usually to ISO. I rip with DVDFab and AnyDVD, and I usually play over the network, although I can confirm the same issue when playing from USB.

The problem occurs whether I rip the full disk with AnyDVD or DVDFab, or rip using "movie only" with DVDFab, and it also happens when playing the original disk via a drive share, using AnyDVD to decrypt the disk on the fly. I don't get the problem if I play the same ISOs using PowerDVD on my PC.

I'll try and get you some more examples of disks where I have the problem, another one I can think of is Harry Potter 7.1.
One hint as to whether a BD might have an issue is to check whether the movie is composed of a single m2ts file, or several separate ones - a single m2ts file means it won't use seamless branching.

did you try to "unpack" the iso file with for instance using poweriso?
to a folder structure with BDMV.
and play that folder on the mini to see if it then does work,
if so then the problem is probably the iso file.

I ask this as i do this to some AVCHD .iso if seamless branching is used in them
and they all work if i unpack them with Poweriso to a BD folderstructure instead of one file.

Where are you attempting to play these titles from? A network drive? Wireless?

Alien
Aliens
Alien 3
Alien Resurrection
American Gangster - Extended Unrated Version
Battle - Los Angeles
Cars
Cars 2
Drag Me To Hell - Unseen Version
Expendables, The - Uncut Version
The Fast And The Furious - Tokyo Drift
Fast & Furious 5
Gladiator
Harry Potter And The Deathly Hallows - Part 1
Harry Potter And The Deathly Hallows - Part 2 - 2D & 3D
Inception
Independence Day
Iron Man 2
Sin City - Recut & Extended
Limitless
Paranormal Activity 2
Paul - Extended Version
Pirates Of The Caribbean - The Curse Of The Black Pearl
Pirates Of The Caribbean - Dead Man's Chest
Pirates Of The Caribbean - At World's End
Pirates Of The Caribbean - On Stranger Tides
Pulp Fiction
Resident Evil
Resident Evil - Extinction
Resident Evil - Afterlife
Salt
Saving Private Ryan - 2 Disk Special Edition
Senna
Star Wars Episode I - The Phantom Menace
Star Wars Episode II - Attack Of The Clones
Star Wars Episode III - Revenge Of The Sith
Star Wars Episode IV - A New Hope
Star Wars Episode V - The Empire Strikes Back
Star Wars Episode VI - Return Of The Jedi
Stargate - Ultimate Edition
Sucker Punch - Extended Edition
Taxi Driver - 25th Anniversary Edition
Terminator 2 - Judgement Day - Skynet Edition
Terminator Salvation - Director's Cut
Wall-E