Simply go to your WorldofWarcraft\Interface\AddOns\sct folder (this is the same location that you would've unzipped SCT to initially). Find the sct_event_config.lua file, open it up using Notepad (which you can do by right-clicking on the file and choosing Open, then choosing Notepad as the program to open the .lua file), scroll down within the file to the lines that show you Counterattack, Mongoose Bite, etc (or do a Find search for Counterattack or Mongoose), and comment them out, which means putting -- in front of it. That's right, just a couple of minuscule dashes.
By putting those two dashes in front of the line(s), it will eliminate them from being loaded up when the code is run. The reason they didn't show up in v4.12 is that you would've commented out the lines already, as they are not commented out by default. As for the reputation gains, I haven't seen any reputation errors, so I'm not sure what to suggest here.
I understand that you're frustrated by the messages and having to update add-ons post patch, but reading the ReadMe file within the sct folder or the information listed in Grayhoof's portal would also give you the knowledge necessary to correct the issue. I have zero knowledge of coding/programming, yet finding the solution is just a matter of looking through the information available. Instead of being unkind and angry towards Grayhoof, the appropriate thing to do is to say thank you. By the way, thank you for such a great add-on, Grayhoof!
In regards to the other comment about only showing the "spam" when the abilities are up...this add-on is meant to simply show the damage that you take, which makes it lightweight. The extra messages showing you that you can use your abilities is an added bonus. If you don't like it, edit the .lua file, and put -- in front of the appropriate lines.