For a while there in the 80s some people assumed there was a second five year mission, before TMP. So you've got some variously interpreted combinations of when the uniforms changed and when the Enterprise was refit. Although even by that logic is seems stupid to have a refit Enterprise with TOS uniforms.
The decisions that shaped cover art weren't necessarily the same as those that shaped story content. Sometimes it may have been a matter of the cover artist only having limited photo references available, or not being familiar enough with the franchise to know they were from different eras. They didn't have the Internet at their beck and call to give them oodles of screencaps and Wiki articles.
Or it could've been for promotional reasons. Early on, the covers were given the look of TMP or TWOK in order to tie into the prominence of those movies, even if the stories inside were set in the series era. Later on, though, sometimes the reverse was done, with TOS-era covers put on movie-era novels (like The Better Man
and Ice Trap
), perhaps because TOS was more perennially popular. Although later covers got the era right more often, so maybe those were mistakes due to miscommunications or lack of proper reference.