I tried this out in my B&A world, and I got stuck inserters. I ran the inserter cleanup tool over the area, which I think is supposed to put a mark on the inserters, but no dice. The train stations have Ultimate Stack Filter Inserters, and the filters on the inserters are cleared as soon as the train leaves. I had the unlock chests option on, but not delete hand contents - those hand contents are valuable. I took a look through the code, but nothing jumped out at me.

Hi,
are the inserters in the selected area modded inserters or vanilla inserters? My mod supports only entities with the type "inserter".

The inserters will only be marked if you activate the following options: Selection: Enable inserter cleanup planner, Selection: Clean up permanently and Mark selected inserters

Please check also ingame, as the setting in a save can differ from the standart settings.

Definitely modded inserters, but they should still be of inserter entity type. I did get the mark to work, after double-checking that option. Although marked, the inserters were still not cleaned. I did figure out that I could add a blacklist filter inserter to remove accidental cargo from the wagons.

If the inserter could not set back the stack in hand to the pick up target and the option to delete the stack in hand is not set the inserter could not be cleaned and the stack remains in the hand of the inserter. This is an intended behaivior.

Sorry to hijack, but it seems related.
First off, I really like this mod, but I noticed something strange.
In B&A inserters can be adjusted to pick up/drop at an angle.
However when I test the inserters will only clean if that angle is 90 or 180 (standard).
If drop is at 45 degrees the inserters do not clean.

Hi Wadash!
To ensure that only inserters that are stuck are cleaned, my mod checks whether held_stack_position is equal to drop_position. The inserter is only cleaned if the two positions are the same.
If a mod changes the angle at which an inserter stops, but does not adjust the drop_position, this inserter will not be recognized as stuck and will not be cleaned.
I would not like to change this behavior of my mod, otherwise there is a risk that when the inserters are checked, inserters that are not blocked at all will also be cleaned.

Thanks for the response.
The benefit of the mod far outweighs this minor thing.
It did take a bit of time to figure out why though, maybe it will help someone else using bobs inserters.
My train stations have been running smoothly after setting all inserters to drop at 180 degrees. (It seems they can pick up at 45 degrees though)

Thanks again for a great mod!