Compatibility of the FTA's remedy rules with the WTO obligation

Once a remedy measure is taken in a way in which the FTA partners would get more favourable treatment than the other WTO Member, is there a legal issue of whether this would be in contrary to any WTO obligation? i.e. if an anti-dumping investigation differentiate between products supplies by FTA partners and other products originated from other WTO Members, is such differentiatation discriminatory under the WTO obligation?

With anti-dumping, the duties are calculated for, and imposed on, specific companies, so there is really no way to treat WTO Members equally. Thus, I don't think the issue would come up. (Unless you mean that one methodology is used for FTA partners, and a less favorable one is used for other WTO Members).

But for safeguards, there are some issues relating to FTAs. It's a bit hard to answer in the abstract, though. There are various aspects of this issue, and it depends on the particular facts.