The file may be broken from a user's perspective (lots of repeated patterns that are not meant to be played) but there is nothing from the software's perspective to understand this, because what the file does is technically perfectly valid. You can remove the excessive references to pattern 0 in the order list (only the first one should stay) and re-save the file, then it will be played as intended.

Yes I know that I can fix the module by editing in a tracker. But the issue is that OpenMPT reports the wrong duration for subsongs. Here is another one: http://modarchive.org/index.php?request=view_by_moduleid&query=125974 The duration for subsong 3 is seven seconds but it actually is much longer than that.

In both modules, the subsongs jump to a pattern that has already been played by another subsong. It's by design that it stops counting once a row is hit that has already been played.

You will find that e.g. XMPlay handles both of those cases exactly the same as OpenMPT does. It's not up for debate to change that behaviour.