He's actually right; it's in the big block of after-text for Cross-Training; it's on the following page and is thus easy to ignore/miss:
You may not choose an ability you already have, and if you later gain an ability you’ve chosen here you do not gain it asecond time; instead, you make a new cross-training choice to replace the former one.
FantasyCraft, pg. 48.
As a GM, I don't see any huge problem with reworking that paragraph to essentially count your levels as X levels for progression (so with sage 4/Opp 8, since BP is an every-fourth-level ability, you'd get BP III, but if at Level 4 Sage you were to take a 2/11/19 ability like Fortunes of War, then 2 level dip into Soldier, I would rule that you don't get Fortunes of War II, but instead you have fortunes of war I and are 6/11ths of the way to Fortunes of War II), but the restriction makes sense.
Generally, that's something I think would be a nice tweak for most class-based things in the system, since I've never liked how you can multiclass into 3-4 classes to get massive save bonuses (since many classes get an instant +1 or +2 to certain saves at level one, but then actually progressing in those classes only gives another +1 every 3-5 levels or so), but if you multiclass between several Med BAB classes, you'll have to take that +0 from the first level is each, dropping you somewhere between Low and Med. If it were simply "add your levels in Med BAB classes to determine your BAB gained from them" and the same for saves and legacy abilities, I think it'd be a lot cleaner for small loopholes like that. Granted that would probably take some confusing or finnicky language, and ultimately it's only a minor issue, but I figure I'd muse on it while it's relevant.
So yeah, he's right. No battle planning III, unless you have a forgiving/allowing GM.