For background reference: I am playing a Mage, and I have tried to make it a point to raise my Luck by 1 and two other attributes by 5 each on every levelup, by raising ten untrained skills and ten major/minor skills governed by the correct attributes on each level. In this way, I have managed to get my Endurance up to 100 already, for example.

However, on my most recent levelup, I initially had 95 points in Willpower and 65 points in Agility; I put on some Light Armor (including a light shield) and let myself get hit enough times to get ten total points, divided among my Block and Light Armor skills. (I think I got four points in Block and six in Light Armor, though that's probably irrelevant).

I was also trying to get 5 points in Willpower to max it out as I had already done with Endurance, and so I practiced my Restoration, Destruction, and Alteration (and no other major or minor skills) in order to do that. Nonetheless, despite leveling up ten skills governed by the Willpower attribute, I could only raise my Willpower by one point on that levelup. (In fact, the only bonus on that levelup was +5 to Agility, which was correct; but there should have been a +5 bonus to Willpower as well.)

In short: My Willpower is 95, I want to raise it by 5 (to 100), and the game won't let me. I didn't have this problem with Endurance.

I remember having this issue before. I got around it by loading the game, training willpower slightly less (so it was a "4" increase) and then leaving it at 99 until later on when I had no other good candidate attributes to raise.

The last point doesn't matter a huge amount, except for appeasing OCD.

This is a known bug and it is fixed, among several others, by the Morrowind Code Patch (MCP). More info on the MCP here.

By the way, the MCP does not replace the Morrowind Patch Project (MPP), because they fix different things, so you should use both.