Drone matches s17e21 to one piece 648 where it is actualy 649.
Could this be because one of the Toriko crossover episodes was given a scene release number but was marked as special number 25 on the TVDB?
Yes, very likely. If its mapped on thexem.de properly it would be correct in drone (when searching). Trakt doesn’t give drone absolute episode numbers, so we generate them based off of non-specials, which works for most, but not all series (where a special was given on).
Quickest solution is to map it on thexem.de I think.
thexem.de marks it properly as far as I can see: http://thexem.de/xem/show/1245
It’s episode 590 which corresponds to special 25. From what I can see the mapping is as it should be.
Okay, I’ll take a look and see what’s going on.
Drone internally treats it (and would in renaming) as 648, but it will search for and import using 649.
Currently drone doesn’t support renaming using the scene numbering (for standard or anime series), not yet sure how we want to handle that.
It’s not a big deal for me as long as it manages to find and download the correct episodes. I’ll just have to turn off my OCD. 
It would be great if at some point you’ll consider making it possible to both use {absolute:000} and something like {scene:000}. People can then decide for themselves which numbering they pick.
Edit: having said that, I just found out that it won’t automatically or manually download new episodes either. When I click automatic search I can see that it finds results but none get put into SABnzbd, and when I click manual search I find 6 different releases though all of them say “Episode was not requested” on the red exclamation mark on that row. If I click download anyway, Drone says “[POST] Internal server error : /api/release” and doesn’t download anything. My error log says this:
System.ArgumentException: Empty collection is not allowed.
Parameter name: remoteEpisode.Episodes
at NzbDrone.Common.EnsureThat.EnsureCollectionExtensions.HasItems<NzbDrone.Core.Tv.Episode> (NzbDrone.Common.EnsureThat.Param1<System.Collections.Generic.List1<NzbDrone.Core.Tv.Episode>>) <0x00063>
at NzbDrone.Core.Download.DownloadService.DownloadReport (NzbDrone.Core.Parser.Model.RemoteEpisode) <0x002b3>
at NzbDrone.Api.Indexers.ReleaseModule.DownloadRelease (NzbDrone.Api.Indexers.ReleaseResource) <0x000cf>
at NzbDrone.Api.Indexers.ReleaseModule.<.ctor>b__0 (object) <0x0002b>
at (wrapper dynamic-method) object.CallSite.Target (System.Runtime.CompilerServices.Closure,System.Runtime.CompilerServices.CallSite,System.Func`2<object, object>,object) <0x000a0>
at Nancy.Routing.Route/<>c__DisplayClass4.b__3 (object,System.Threading.CancellationToken) <0x0013b>
Ahh, found the issue, pushed a fix.
That does indeed seem to fix the download issue I had. So there’s just the disparity between scene numbers and the absolute numbers that Drone uses, but like I said I think most people can live with that for a while as long as the episodes keep rolling in. 
Yeah, that one has a card on Trello already: https://trello.com/c/jbLZBx3G/268-allow-users-to-choose-how-they-want-their-episodes-stored-on-disk