Hello @DenizTC and welcome to the community.

Yes, order matters in the CODEOWNERS file, specifically lines that come later override lines that appear earlier in the file. In the example in the documentation, this is taken advantage of by starting with the least specific rule and then following with increasingly more specific rules as in this excerpt:

# These owners will be the default owners for everything in
# the repo. Unless a later match takes precedence,
# @global-owner1 and @global-owner2 will be requested for
# review when someone opens a pull request.
*       @global-owner1 @global-owner2
Order is important; the last matching pattern takes the most
precedence. When someone opens a pull request that only
modifies JS files, only @js-owner and not the global
owner(s) will be requested for a review.
*.js    @js-owner

Is grouping by teams not the correct thing to do?

It isn’t specifically incorrect but it may mean that you’ll have to write more rules to achieve the same effect than if you worked with the way the CODEOWNERS file is interpreted. So you may want to reorder your file like this to achieve your stated goal:

# PD files
/engn/headers/pd* @ORG/team-b
PD exceptions
/engn/headers/pdSql_file1.in @ORG/team-a
etc ...