Might be, the counters are a later addition and may have some false positives. I'll take a look.
oh ya, I noticed that you missed the EXP display fix for Reyn's 1st level and the 1st encounter in v1.03, so, just wanted to leave a note as a gentle reminder.
There is also the master counter in Falgar's Palace (which I believe is a different map than Falgar's Abode? since the counters and travel points are different)
For the optional scenes, I was unable to find 1 in Rok's Fort (I did find all 15 Masters and did the scene with Jason/Rod). I just started a 3rd run and will check again, along with the Treasure counter.
EDIT: Sorry, my error on Fort Langley and Stahl Dam, updated my comments above in case you saw an earlier comment. Additionally, on my 3rd run, the counter started at 2, and reduce by 1 after I did the scene with Jason/Rod (and I talked to both).
EDIT2: On my 3rd run through, I noticed something interested...in Path to Falgar's Monastery, the Master counter did not decrease when I first recruited the Snake Demon master, but went down after I activated the portal and went through it. So, I am not sure if the Fort Langley and Stahl Dam counters could be not going down correctly due to something in the way the script checks for the Master counter.
The fort and dam counter is fixed, but I haven't uploaded the update yet. Sometimes, re-entering the scene is needed for the counter to go down, so that's what happened with the Snake Demon.
I took a look at the scene counter in Rok's fort, and I had a typo in one of the strings that checks for the T-Rex scene. Will be fixed in the next version.