Pilot reported an MEL for a below flush brake wear indicator pin was not in compliance with the General Procedures Manual. Also reported were instances of changed or missing log book items.

Narrative

Please see my [report] dated XXXX.This new [report] is about the same AML problem on a different airplane in [Report] XXXXX. The [Report] XXXXX reflects three different [tracking] numbers that disappeared or never made it into records.Please note that the [Report] XXXXX [tracking] numbers were missing out of the system until the [report] committee investigated and then the [tracking] numbers/Maintenance entries were inserted into the system.NOW ON TO AIRCRAFT X....DATE...This aircraft I found the number 4 brake wear pin indicator below flush. This Brake was on a previous TAC...XX-XX-X to be replaced within 3 days or a Maintenance base overnight.....My issue was the fact that the wear pin was at least .015' below flush. 737 brakes are only deferrable down to flush; not below flush per GPM.My first argument is or/was that if the brake wear pin is below flush on a prima facia find; on my flight; it would not be deferrable by the general procedures manual; therefore I refused the aircraft. (Interestingly.....the flight cancelled within just a few minutes of me advising dispatch.)I ask please that the review team not get overly wound up about this below flush issue; as much as the potential [tracking number/maintenance tracking program] disappearance malfeasance....even though I cannot find; through Maintenance Personnel conversations; what a minimum brake thickness would be to render the aircraft unairworthy.Again; please; this [report] is not as much about the below flush issue as the following [tracking number] entry discrepancy similar to my previous [report]. The below limits wear pin; is an issue THAT REQUIRES INVESTIGATION.......but I don't personally want the review team to be distracted by only an issue of a below limits brake wear pin.The [tracking] entry number for the brake that I wrote up is LP (Logbook Page) X. On that same AML page there was number LP Y (actually correctly put in [logbook]).....an entry about a below limits tire that was properly addressed via a deferral and subsequently a tire replacement..... this is why I need to point out that I am not going to believe the fact that a derogatory entry (LP Y) was 'forgotten' to be put in the safe system; because another item on the exact same logbook page WAS entered properly...... This same thing occurred on my previous [report] XXXXX; mentioned above; regarding other non derogatory entries on the same logbook page making it into [logbook]. The next entry (actually put in [logbook]) is number LP Z; which was my refusal of the aircraft referencing MIC number LP X.For several days I checked all three of my Aircraft X logbook entries and found that in the computer system only the last two; non derogatory AML entries were in the computer. Missing was only MIC LP Y......This missing MIC LP Y situation is very similar to my previous [report] issue; mentioned above; where the derogatory MIC entries did not make it into safe until after my [report] was investigated.Anecdotally; just a couple of days ago I noticed that there was a MIC LP Y in the system.....Somebody transposed the information for another MIC item into the MIC LP Y entry concerning another Maintenance issue on. Aircraft X....Someone then did make a correction on another [tracking] number and corrected this information by referral; but not not an actual change to LP Y.... In other words; a reference to an incorrect entry to LP Y....; but my concern is now there is still an open item [tracking] number LP Y that was never addressed in the computer system; and out of FAA and other pilots view..... I believe by intentional design.....and it's my belief the the sign off to this [tracking number] was not a legal sign off as well; due to the brake being found below flush.My accusation and assumption here is potential Maintenance malfeasance to cover maintenance tracks for trying to sign off a potentially illegal deferral on the number 4 brake.I have it on firsthand authority from a unionofficial; that other captains have also complained about missing entries when they go back to look at recurring items on aircraft that they have flown.I am stating that my belief is this is endemic to 'hide' potentially incriminating logbook entries to cover potential errors by Maintenance.Stop maintenance malfeasance and educate mechanics on their own manuals.