OK, so this is kind of odd. I've done this only one time over a year ago, and do not recall this quirk happening. I've got the book and the house in Whiterun (Breezehome) with the alchemy lab for the bookshelf (only option when removing game update back to no patches as Hearthfire requires one and barrels don't seem to work). I can do the cycle of "activate bookshelf", "read book within bookshelf menu", "pick path", "close out of book but not the menu", "place on shelf", "exit and take without reading", and then rinse and repeat.

It raises the skills each time, yet trying to raise magic skills only to create a sub save with enchanting at 50 then another with it at 100 (want to try some experiments to pin down the "threshold" for the restoration potion glitch to not terminate progress), I discovered an oddity. Destruction and another skill were at 99 not 100. I thought "Huh, weird. Oh well, once more," and repeated the magic path. It failed to raise them one point more. I seen that the first save at 50 enchanting I made had destruction at 49, not 50, so it had begun before that point.

I went back to my save before starting and redid it watching the values this time carefully. They were a Breton's start values with none advanced during play by even one (though destruction had some little experience on the bar): alteration, illusion, and restoration at 20, conjuration at 25, destruction and enchanting at 15. It went normally all the way to those last two (destruction and enchanting) going to 45. Then I saved. I did the next iteration and sure enough, all the others went up by 5, but destruction only raised 4 to 49. I reloaded and tried again with the same result. I went all the way out to the title screen and reloaded (some oddities can seem to persist when you reload from game rather than that screen). No change.

I have been googling and trying to figure out search terms like "one skill" or "skill didn't" and the rest to nail some mention somewhere of the oghma doing this. It wouldn't even necessarily have to occur while doing the oghma glitch (if it can raise a skill by 4 instead of 5 then, surely the error could happen in a one time use as well). But I have had no luck. Has anyone ever seen this happen or heard of it and if so, is there a cause or workaround (pay trainer for one raise came to mind)?