I noticed this early on, but also wasn't sure if it was a bug or not--good idea to list it though.
Correction:
In my current campaign, I noticed that in provinces where I had higher level specialty buildings allowing me to recruit a level 2 or 3 agent, I also got a retainer selection. In other words--if I was getting to add 4 skill points at recruitment, I also got to add a single retainer. I had this ability for both a monk and a Ninja. This makes me think that not having a retainer choice for recruitment at only one XP step above entry level may not be a bug.
Cheers
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