I just went to Vilkas to get some Two-Handed training. I was at Level 84, paid 5 times, and finished at Level 88.
So I restarted and got 85 (paid), 86 (paid), 87 (paid) 88 paid but without increasing the level, so still level 87!
And then the last one 88 (paid) and increase to level 88.

So I took 5 lessons, paid them all, but increased only 4 times.

And I remember that earlier at level 30 I had the same problem with Restoration (I think) but I didn't counted if it was quite right and continued. But I remember that I thought: I didn't hear the noise after that lesson..

Now I restarted 3 times, even leaving the house and waiting a few hours. Result is the same: Paid 5 lessons and got only 4 increments in 2-H skill.

Did you have the same problem?

it is safer to pay one and wait for the message to disappear, then pay for another and wait and so on.
sometimes quests have the same problems when you skip dialogues, you can end up with a completed misc quest that's still showing on the quests menu.

It's what I did. I waited. But no way... Still the same problem.

It's not so much a question of money but I can train only 5 times and now it gives me only 4. At level 74 it's getting hard to level up. That's why it's so annoying.

It' will level up when you reach the next level by using it in combat. I had this problem on my first character, but went away as soon as I leveled up, it just caught up with me all of a sudden.

idk then, it always happened to me when I bought all 5 in a row fast. and never when waiting for the message to disappear.

@ Bartoman: Thanks for your reply. But my problem is that I have really waited. And the other 3 more times even more longer. So it's a bit bugged. But as JiSoo says it should come together with my next self training increase. Thank you JiSoo.

As I'm now at Level 74 I prefered to reload and take 3 lessons with Vilkas and 2 in Archery with Aela. I have 100 almost everywhere except Destruction 95, 2-H 87 now, Lockpicking 98. I have only Archery 56 to increase for getting at higher level as my pickpocket 20 and sneak 37 will remain like that. I don't like sneaking (hate) and I don't steal or pickpocket, even if it's to replace items back. I prefer to train myself in Archery though it's not my cup of tea.

Before starting a new char. I want to explore more Skyrim.

At least with those NPCs, if you've finished the Companions line and have them as followers, you can open their inventory and take your gold back. Makes the missed level a bit less painful.