My ships get bombarded from colonies of European nation (Portugal in this case) I am currently at peace with. In the attached log you can see two combat events.
FreeCol game version: git-20200715 (Revision: 8baaf7a)
FreeCol protocol version: 0.1.6
OS name: Windows 7
OS architecture: amd64
OS version: 6.1
The log file shows two combats where a colony bombarded a Privateer. This is WAD (working as designed). Privateers do not fly your flag, and every other colony is hostile to them.
Closing/not-a-bug.