I must say that I have ignored the metric sizes so I haven't noticed that.
Are you seeing 2.4mm and 2.5mm both referencing to a #40?
They are both very close but the 2.5mm is closer.
3/32 = .0938
2.4mm = .0945
#40 = .0980
2.5mm = .0984
A 2.4mm is smaller than a #41, which is .0960
I have not come across any plans page that calls out for a #41 hole so if I were using metric I would stick with just one, and it would be the 2.5mm. The difference is literally a rounding error when measuring to 1/1000 of an inch.