This is a long shot, but is it:
The letter 'k'
Using one of me is common in science and other areas,
k could be many things in science, such as a variable or a prefix to a unit.
but in other areas they sometimes use me the wrong way
'k' is sometimes used as an informal abbreviation for 'okay'.
Using two of me is taboo in science, unless one of me is larger,
If 'k' is a variable, it would not be good to name two variables k as you couldn't tell them apart, unless one was lowercase and the other capital. If 'k' is a unit prefix, there is no unit 'kk', but there is the unit 'kK' (kilokelvin).
but in other areas they abuse me again by using two small variants of me
The word 'kk' is also used as an informal way of saying 'okay'.
Using three of me is taboo everywhere.
Three k's would represent the KKK, a racist organization.