Mueller's original scope was russian meddling in our election. When additional evidence came up beyond this scope (i.e. Racketeering), FBI agents no doubt reported their findings. Typically a new scope gets opened and such investigations drag on. That's the nature of such undertakings whether it be watergate or the IRS investigating a random individual for tax evasion.
Although collusion was the entry pathway to the investigation it may not be the charge that will be most problematic to trump.