so i increased my int mod from +3 to +4 and i got an extra skill point for that level, but the next time i leveled i did not get the extra skill point. Usually its a premante increase but I'm not sure if its different for pathfinder. Has this happened to anyone else?

I don't know why but it seems that INT skill points are give every two levels.
I have Human Male Fighter with 13 Int and i get 4 skill points every uneven level and 3 points on every even one.

You gain extra skill points equal to half of your INT mod each level. With an odd INT mod, 3 for example, this manifests as you getting 2 points on odd numbered levels, and 1 on even numbered levels--effectively 1.5 per level. For a mod of 1 it's a 1/0 split, for 5 it's 3/2, and so on.

What likely happened is that, on increasing your INT mod on an even level up, it gave you an extra point because that's normally when you would have been on the lower end of the split, but now it's evening out.

Alternatively, if you got fewer skill points on the next level up, did you take a level in a different class? Because different classes get different amounts of skill points.

If neither of the above, it's probably a bug.

It is weird as my pathfinder rulebook says:
Skill Ranks per Level: 2 + Int modifier.
Of course in case of human it is 2 + Int modifier +1 for human race, But nowhere i can find +1/2 Int modifier so it is probably a bug.

That's for the PnP game, where there are dozens of skills to choose from, not eleven. The skills in this game seem to be loosely based on the consolidated skills in Pathfinder: Unchained, which also do the +1/2 INT mod.

Aha. I'm glad I saw this thread. I'd been wondering if I'd been hit by some wierd bug when I realized my Magus didn't alweays have the same number of skillpoints every level.

I've also noticed that skillpoints are retroactively awarded to you for previous levels gained when your INT mod is permanently increased. Is that from Unchained as well?

I asume that because it's using something similar to Pathfinder : Unchained's 'Consolidated skills', it makes the same changes to skill points as that alternative rule does.
In the normal Pathfinder, there are more than twice as many skills, so in a way, each skill point in 'Consolidated skills' is worth at least twice as much, because it can be applied to at least twice as many situations. So to balance that you get 1/2 level skill points, instead of 1 level skill points.
Hope that makes sense.

You can see the 'consolidated skills' rules here:
http://legacy.aonprd.com/unchained/skillsAndOptions/consolidatedSkills/index.html
See especially the 'Class skills' sub-heading.

Compare with the standard skills from the core rulebook, here:
http://legacy.aonprd.com/coreRulebook/usingSkills.html
See especially the 'Aquiring Skills' sub-heading

Now I'm not saying that's exactly what they're doing here but I think it's the broad outline of their approach.