If you're using ports, you need to (well, really, really, really should) have an upper-level schematic that has all your schematics as sheet entities, and defines the interconnections between each sub-sheet.
Anyways, it sounds like you're looking for the "Synchronize Sheet Entries and Ports" menu option:
You can also update each schematic symbol individually by right-clicking on the schematic symbol on the top-level document, and selecting "Synchronize Sheet Entries and Ports" in the menu.
I'm not entirely sure if this answers what you're asking, as you're describing it in a way I haven't heard before. If you can post the exact content of the project compilation errors, I can probably be more specific.
If you're using schematic ports to connect separate schematics without a upper-level schematic containing each sub-sheet as a schematic symbol and wires to dictate symbol interconnectivity, well... you're doing it wrong. You should be using off-sheet connectors for that (but that's a terrible way to define inter-sheet connectivity anyways).
Edit:
From the OP's comments below, it sounds like the issue is the error checker is complaining that if you have multiple schematic pages with ports specified as "output", that are connected together, this will produce an error. While this error can be very useful, there are many situations where you do want to connect multiple outputs together (Think of multiple SPI slaves. The outputs are tri-stated until CS is asserted).
The generation of interconnection errors are generated by the settings on the "Connection Matrix" page of the "Project Options" dialog. You look for the box at the intersections of the two pin or port types you want to modify the reporting for, and then clicking the box cycles through the possible error or warning generation options.
You probably have edited the the schematic symbol in Sch library after placing its footprint on the layout design.
In situations like this, you need to update your schematic design from library (Tools/Update From Libraries...), then update your PCB with the updated schematic. If problem still there, remove the footprint from PCB file and update the PCB file with schematic again.
Also make sure the symbol in schematic sheet has the same footprint model name as it has in Schematic and PCB libraries.
Best Answer
Your 'Designator' fields on the schematic symbol pins have to agree with the pads on the footprint. Otherwise, how would the program know where the pin numbers are on the footprint?
You can make the 'Display Name' whatever you like- it's just for human use.
Where you have PA0 etc. one would normally have the physical pin number, matching exactly the pin numbers on the footprint.
You can fix it by editing each of the schematic pins, and that should do it, if your footprint is numbered correctly.