@HarryT: Deleting highlights or notes from anywhere in the UI will not have any effects on MyClippings.txt because it functions like a simple (event) log file. "The system" will record there that something was added but it will not even record that something was removed let alone remove the preexisting record.
@Phil Wolff: If you can't eliminate creating of those unwanted / accidental highlights you will probably have to switch from parsing MyClippings.txt to parsing those files in associated ". sdr" directory for each book (I can't remember what were the extensions matching each book format, IIRC for old mobi format it was ".mbp") in which Kindle stores "active"/up-to-date record of that book's notes, highlights and last-page-read.
But you would first need to figure out the (binary) format itself and type of encryption used.
Possible starting point on that topic (even if that app no longer works for files produced by newer firmware) :
http://www.angelfire.com/ego2/idleloop/mbp_reader.htm
Failing that I don't see any other alternative other than doing something tedious like beginning or ending all your intentional highlights with some unique string of rarely used characters and use that as a "helper markup" to later be able to filter out (un)needed information when parsing MyClippings.txt.