In my experience, I haven't had that particular bug show up.
So, let me get this straight, when you try and delete an item via the Modder, you get that error? And does the error appear when you press the button? When you mess with any one of the comboboxes?
I'd like to know which item in particular is the problem though, to publish a fixed version.
In any case, if the app still won't let you delete it, you could always go the ugly-people route and delete it via SQL, you just need the sort_id, which will be readily available from the generated text report.
Code:
delete from dbo.MarketResource where sort_id=[Your Sort ID]
My suspicion is that it's the Item XML that's the culprit, I
might have modified it after publishing the last version, I'm not sure, tbh.