There is no lore reason why this is the case. There are multiple races that get extra skill proficiencies. Half-Elf's default racial features include skill versatility, which gives extra skill proficiencies. BG3 is using a variant rule from the Sword Coast Adventurer's Guide that allow you to replace skill versatility with an appropriate racial trait from your Elf parent, which is good, but for some reason they haven't put the default feature of skill versatility in.
Selecting extra skills in general seems to be giving the game engine trouble or is being difficult in some way, I've noticed that features giving extra skills seem to misbehave, or not assign skills correctly.
