Hi, just did a quick scan.
The main problems I found were:
As has been mentioned above, the following maps have zero length reject data:
E1M1, E1M2, E1M3, E1M4, E1M5, E1M7, E1M8, E1M9, E2M1, E2M2, E2M3, E2M4, E2M5, E2M6, E2M7, E2M9,
E3M1, E3M2, E3M4, E3M5, E3M6, E3M9, E4M1, E4M2, E4M5, E4M8
An empty / 'all zero' reject lump of the expected size is preferable to a zero length reject.
E3M3 - Side 522 references missing texture '-CKRED1'
E2M2, E2M5, E3M1, E3M7 - Have zero length segs and duplicate seg vertices (nodebuilder issue).
E3M4 - The yellow key is not needed, the yellow door opens without it.
E4M1 - The red key isn't needed, the red door (sector 93) needs the blue key to open it.
E4M2 - Line 1012 (S1 Door Open Stay) has no sector tag.
E4M9 - Sectors 305, 307, 308 have less than 3 lines. Also this map has 2 player 2 starts and no player 3 start.
Other minor problems:
Maps with DB starts (not a problem due to skill flags): E1M4, E1M5, E4M5
E1M1 - Thing 87 has no skill flags set.
E2M1 - Thing 49 DM Start on Cacodemon.
E2M9 - Thing 87 has no skill flags set.
E3M1 - Thing 51 DM Start on Imp.
E3M5 - Thing 180 DM Start on Sergeant, Line 243 has a special and tag but is not linked to a sector.
E4M3 - Thing 336 DM Start on Sergeant.
E4M5 - Thing 394 DM Start on Demon, Lines 1485, 1488 and 1490 have special and tag but are not linked to a sector.
E4M9 - Thing 330 has no skill flags set.
I will try playing through it if I get the time.
Hope this helps.