As an update, the issue is still occurring. Here are the results of the testing I did.
I removed my WTF and Interface folders. I logged into WoW and let it rebuild the folder structure and contents then exited and closed the game. I installed a fresh/latest version of the Guide via the installer. I then logged in and checked the tracking menus (Guides and WoW’s). I am using Stormwind as a test area for it’s ease of access and small number of pets. I set up the options so that I am tracking pets via WoW’s options and also choosing to only show Not Collected pets via Guide Options on the Maps. Currently, the icon for the Stormwind Rat shows on the map and states I have not collected it.
I made sure to open and close the Pet Journal. No change.
I left the Stormwind zone and re entered it. No change.
I entered a pet battle with a Stormwind Rat and forfeited. No change.
I entered a pet battle with a Stormwind Rat and caged it. The map shows correctly now.
I inspected multiple zones and checked what was shown as Not Collected vs my Pet Journal and it was all showing properly now. For completeness, I logged into several other characters and found them all to be displaying collected and not collected properly.
It appears that the information did not get saved/updated/requested in the Guides database until the pet battle event of successfully caging a pet occurred. I’m not sure what event the Guide looks for to update it’s database.