This is timely for me, I was thinking of making the very same thread a couple hours ago.
My list in no particular order:
Stance on higher education
WWI starting early (I.e. before the last days were supposed to start in Oct.)
The switch from 1914=Armageddon to 1914=last days made after nothing happened.
What's all this I hear in hushed tones about 1975?
If we're supposed to be gathering together "all the more so as [we] behold the day drawing near" why are meetings/conventions/assemblies being shortened or eliminated?
Similar confusion on the reduction in the requirement for pioneers
They'd talk about how Satan can influence us through the lyrics of worldly songs one week, then go on and on about how important it is to sing along at the meetings the next.
Apostate paranoia (surely if they deal in half truths and lies, they could easily be shown to be wrong)
DFing (my hard to silence doubt was "that seems like something a cult would do... But I guess it's scriptural so it must be for a good reason")
The whole system of rules around dating always seemed designed to lead to kids getting married before they're really ready, and that certainly seemed to be the end result.
While I accepted the blood ban the exceptions (vaccines and later fractions) never made sense. That being so, I was still glad to take advantage of the exceptions if needed.
The fact that I'd practically have to be lobotomized to enjoy paradise, as essentially all of my hobbies and interests rely on stuff that's never been depicted in the pictures of it. Not to mention the whole being vegan thing...
When they added credit/debit machines at the assemblies and conventions after my entire youth was spent listening to them rail against churches in Christendom for having ATMs in the lobby.
The "running of the bulls" and many other arrangements around the conventions and assemblies seemed to lack the love that was supposed to be characteristic of true Christians.
Counting and printing service time and announcing pioneers seemed to go against the counsel to not let your left hand know what the right is doing
The impossibility of the Noah's ark story
Evidence that humans didn't originate 6000 years ago in the area they identified as the garden of Eden
There never seemed to be any prophesies that were fully understood before their fulfillment
The violence in the OT never sat well
I think I could keep going, but the longer this list gets the more embarrassing it is that it took me so long to wake up.