It is a bit odd. If your number is the "call if found" number, because you already know he's hard to reach at work, then maybe she didn't figure there was much point in calling him at work either. Maybe she wanted to know who he chose as his "go to" person - then when she realized it was a) his mother and b) someone she knew, she relaxed and started chatting.
If they are together, no, she shouldn't really "go through" his phone, but he shouldn't have secrets either. If they have trust issues, it's between them, not either of them and you.
I'd mention it to him about how funny it was to get a call from a number you didn't recognize, and to have her call a number she didn't recognize, and lo and behold, there you were on the phone together. See how he reacts. If he has a reason to be concerned about her, you'll have let him know. If it's fine, you'll have a little laugh. Otherwise, they are adults, and you have to leave their relationship and privacy issues to them.