Firstly - I think you have the right idea - the remarks on your work permit probably do indicate that you received it as a PR applicant ("APR pending" or words to that effect).
There are many ways someone can be eligible for an open work permit, and indeed there are several ways a spouse can be eligible. See Who can apply for an open work permit? (http://www.cic.gc.ca/english/helpcentre/answer.asp?q=177&t=17).
You'll notice that the above list includes spouses of skilled (NOC 0, A, B) workers, and I guess they assumed you were applying in this category, without further information to go on.
The list does not specifically include spouses of BOWP holders, but the manual on bridging permits does (http://www.cic.gc.ca/english/resources/tools/temp/work/prov/bridging.asp). When you reapply, quote them this section of the manual and make it clear that you are a BOWP holder and a CEC applicant.