The BG2 engine will allow a newly created fighter class player character to have four points of weapon proficiency in the same weapon at level 1. Originally BG1 only allowed up to two points to be put into a single weapon proficiency at the start of the game (despite the fighter having four points in total available); further points had to be added later while progressing in the game. The position in vanilla BG1 is more consistent with the AD&D second edition PnP rules, where the 3 higher levels of mastery could not be gained until higher character levels had been achieved.
There is no problem when the BG2 engine is used for BG2 itself, as the player character will be of a character level where he/she could have access to the higher weapon proficiency levels under the PnP rules. It was probably for this reason that the original designers never thought to address this issue.