AniDB

[15:48] > !watched 3200 all
<@Chii[AR]> WATCHED: there are multiple files for this ep, ignored: 3200 1 - fid/version/filetype/group: 195393/v1/avi/none, 290069/v2/ass/Lupin Gang

[15:51] > !watched Hi no Tori: Yamato Hen all
<@Chii[AR]> WATCHED: there are multiple files for this ep, ignored: Hi no Tori: Yamato Hen 1 - fid/version/filetype/group: 195393/v1/avi/none, 290069/v2/ass/Lupin Gang

I think it says it all

that's no bug. as you tried to mark 1 episode watched "all" doesn't apply