I do believe that there is a problem here.
I first noticed it with the upgrade from RC2 to RC3. I got the same message in a mission that worked fine in RC2 but gave this message at all HB's in a mission that had free standing HB's and spawn placeholders. I posted this mission in the RC4 bug reports but as yet nothing heard.
Since then, I have spent a good deal of time trying to isolate the issue. For example, I find that starting with just one of the HB's (free standing- or carrier if you wish) active and adding each HB one at a time I can get normal spawning until the very last one (7 in total) and then I get the "No available spawn places at this base" showing at all of the mission HB's.
I can only assume that free standing HB's (or carrier HB's) have some sort of total limitation on spawn places for any particular mission. In my mission, I had 7 free standing HB's with 70 spawn placeholders in total.
Interestingly, I can get my mission to run normally by making one HB a regular HB.....but just to throw a spanner in the works....it will only air spawn even though the airfield has dedicated parallel runways on the map!!