Yep! It happens, especially in the habitats of journalists working in areas of civil unrest. My passport cover has almost scrubbed itself completely off from the constant removal from pockets to passport control, back to pocket and several other times it is required for inspection.
When you land at your destination – you will undoubtedly repeat this again and again at checkpoints. Though having purchased a cover from Amazon, it will be taken out from the sleeve to be scanned at arrivals – the problem persists but you can slow it down.
Damaged and/or unrecognisable passports can be refused and this smalltime investment is worth it in the long run. The last thing you need is an unwarranted interrogation and a case of the theatrical good cop/bad cop routines.