Act 1:5 For John truly baptized with water;

This verse helps us understand what Jesus means by being "baptized"  (explained in more detail in this article). "Baptized" is an untranslated Greek word that means "dipping." The phrases describing baptism as "with water" and "with the Holy Ghost" are very different and nether as the preposition usually translated as "with."  The "with" in "with water" comes from the dative form of the word water, which means "with" in the sense of water being an instrument. However, the "with Ghost/Spirit" is from the preposition that primarily means "into" but can also mean "with" in the sense of "along with" and "by" in the sense of "near."

The verses does have the preposition usually translated as "with," but none of the popular English translations actually translated it. It is used with the "days" phrase and means "after" when used with periods of time.