I've only built up three frames previously so I've still much to learn and have never encountered this. Currently building a new frame.
The non drive side BB cup will not go in the last 3mm. Well, it might go in a bit more but it would then be proper man-tight and I fear it would never get it out.
BB cups go in fine up to that point and the thread is not threaded. All the internal thread is being used with it 3mm out. Drive side one is fine.
Any suggestions? Or will it be fine as is? Thanks