UPDATE: I’ve found something here
I noticed the URL generated in the ajax call with path /click/track uses an out of date slug which was changed during the life of the target Topic - could that have affected it? I know most code should rely on the id only, but is this an isolated case where it requires the slug to remain the same as when the link was created in order to work?
BOOM, that’s the problem!
Update the old slug in the source link to the new target slug and the counter appears.
The counters fail because the slug has changed - I think this should be fixed if possible as this should not be a dependency?
WORKAROUND: Update the source link to the new target slug and the counter starts working! @tophee @sam
Unfortunately this is a lot of manual work and you need to identify each mismatching link. A fix to remove this dependency to rely only on the id would be lovely 
Would be also good to check:
- if the bug affects the ‘arrived from’ counters in the post footers.
- if adding a mid post location with a heading at the end of the url breaks the counter code e.g. #heading–myheading because I’m not seeing any counters on those types of links …