Docking Port Bug

1. In-Universe fix: Get KIS/KAS and send Engineer in a shuttle to fix it. You can strut it together on EVA or remove/replace/add parts as you see fit. You can even use explosives if you are angry enough. It is wildcard fix for all other issues as well. (Heck, you can even build cube-sats in orbit with it ;)
2. Out-of-Universe fix: Check docking port state in save file, Acquired state on port might prevent it from docking (bug). Changing it back to Ready should fix it. Example of this operation can be found in famous Duna, Ore Bust!

If you have problems to find part entry in save file, which is very probable as it is big and ugly, try following check-list:

1. Backup previous saves for safety.
2. Start new empty test game and launch your module (just put it on launchpad).
3. Save your test game and use its file for reference.
4. Find broken ship in save.
5. Heal it with content from test save.

Note: do not use quicksave.sfs for manual repairs as game can overwrite it suddenly. Other than that, it is safe to perform repairs with game running in background.

Example of reinforcing structure with KAS/KIS:

Rover loaded to cargo bay, however without any safety locks it will be destroyed during takeoff. Fuel pipe will be used first as it will merge ships into single entity (for some reason struts can't do that). Then struts will secure rover in place.

After mounting hard points on cargo bay wall and on rover itself Kerbal can connect them with pipes and struts.

Liftoff!

Cargo plane and KAS/KIS rover added to my SE.Gaming KSP repository