I just noticed something while updating Spigot to 1.12. The Update was working fine but I had the old 1.11.2 JAR still in my server folder. Unfortunately AMP run MC with the 1.11.2 after a restart - whatever the reason was, since 1.12 was still selected as JAR.
Nevertheless I deleted the JARS from the MC folder and ran another update on Spigot latest Stable but I got both versions: 1.11.2 and 1.12. After playing around a bit, I noticed I had to clear the spigotbuild folder from all jars (except for the BuildTools.jar of course) then only the most actual version would be copied to the MC folder.
Maybe it would make sense to implement the remove of the files before compiling a new one. For linux based OS you could do it the following way:
In the spigotbuild folder within the MC folder
find . -maxdepth 1 -name "*.jar" -type 'f' | grep -v "BuildTools.jar" | xargs rm
Kind regards, Rac00n