Trade agreements often have dispute resolution clauses. These define the institutions and processes to resolve disputes. These would normally be of the form of an arbitration committee that is there to sort the mess out. If nothing else is available the normal fallback is the dreaded World Trade Organization rules.
All of these processes are like any pseudo-legal process : long, expensive and painful for all involved. This is why trade negotiations tend to take a very long time to conclude and why they tend to be extremely detailed documents (or sets of documents).
It's not uncommon for nations to start mini-trade wars, usually involving tariff impositions on a tit-for-tat basis, to try and bully each other into giving in. These rarely result in anything but unemployment and usually end up being resolved quietly by diplomats, having been started noisily by politicians purely for domestic political reasons and not for any realistic purpose or objective.