It seems that some people ended up with duplicate relics in the saved data for our addon… not sure how it happened, must have been a bug with the transition from pre- to post-crucible versions of the addon, and that causes it to think there are extra relics sometimes.
You can try deleting your AskMrRobot.lua settings file in your World of Warcraft WTF/account/[your account name]/SavedVariables folder. (Make sure to completely exit WoW first.) That will completely reset our addon, and usually resolves the issue. Note that after doing so, you will need to reinitialize the addon for each of your characters (open bank once, activate each spec once, open the artifact UI for each spec once, open the crucible for each spec once, and preview all relics once). Then it stays in sync automatically thereafter.
As for not recommending the relic swap, that is because of our new “score threshold” feature (described in more detail here: Best in Bags Feature: Score Threshold). In short: that relic would only be a very small estimated DPS increase, so the optimizer says you can go ahead and skip it if you want.
You can change your score threshold in the filters/options (the filter/funnel icon in top-middle of the screen next to the gearing strategy). It defaults to 0.5%, so any relic/gem/enchant change that would be less than that is skipped. You can set it to Disabled if you don’t care how small of a change it would be.