I am having these exact same issues. Cant claim my TOS enterprise as it tells me "The price for this item has changed." And I pulled a Temporal Escort for a new character and I can only put weapons in 2 of its 3 forward weapon slots.
Im having the same issue in the Deferra zone, warping into system and beaming down to Raveah 2, and im all up to date as well. Not sure how to correct this yet.