Dates don't mean a whole lot with fender, they have a history of using necks, bodies, parts etc to make guitars and basses years apart. Heck, there's a rumour fender Japan guitar/bass necks and bodies which didn't make quality control where shipped to India in the late 80s and then sold as Sunn, Squier II and Encore basses.
So a fender Japan bass with 89 serial number, actually assembled in 90 seems reasonable to me. The 89 part on the neck would be the year the neck was made, probably left on a shelf of necks, and finally assembled in 90, hence the 90 on neck heel and neck pocket.