After you distribute your stat points, there is a checkmark button on the bottom of the stat window, which can be obscured behind the UI at the bottom of the screen, depending on game resolution. You can click on the window and move it up.

screenshot of the stat window (showing initial, levelled, distributed and confirmed stats).

Unfortunately, as you found there is a bug where if you save the game and reload it, any distributed but unconfirmed stat points will be lost. In that case, you can use iZakaroN's SaveEditor (listed below the disk version patch and item editor) to give yourself back those stat points (5 points for each level that you went up, assuming you distributed and lost them all).

If you wait long enough for any food/potion/spell effects to wear off and remove all equipment with stat bonuses (or make sure to take them into account), then the sum of

strength + agility + intelligence + constitution + any unassigned stat points

should be equal to

40 + 5*(Character Level) + possible other bonuses you would only encounter if you explored a fair bit away from Aleroth


There is a description for how to use the editor on the web page, and at level 5 you can add up your stats and unused stat points (neglecting equipment bonuses), and at level 5 that should total 65. The difference between that and what you have is what you use the editor to add. If you didn't apply any stat points at all, you should have 20 free stat points.

Let me know if you have any problems, and I can go through that part in more detail, or zip the data.000 file in the save folder and email it to me (raze@larian.com), or PM a Dropbox link, or something.

There are more than enough stat and level bonuses in the game to make up for the one place you can get a stat penalty (well, there is one thing that can give a penalty or bonus, but quicksaving before that ensures a bonus).
Most commonly the penalty is 3.