I cannot think of every example off the top my head, but Weskers Report (yes that old classic) references events of Gaiden and Wesker claims Sherry in his hands, Capcom still to this day keep referencing that, in Archives II for example despite other material and also games like Darkside making clearer Sherry's fate.

I seem to remember Kirk was meant to be a rookie pilot in training and no prior military experience, yet he reappears (you know what I mean) in Revelations which is set years prior. Might possibly have been archives II that stated he was a rookie, I just read through stuff once out of random interest as a RE fan so don't remember all sources for stuff I read.

The inconsistancies/plot holes in RE5 is due to the moving of dates, it creates a massive gap in time where nothing happens and events that happen just prior to this gap leave gaping questions, like Reapers running loose in the missile area for 9 months, completely unrealistic. They were never researched further like was planned and the file you find implies Uroboros was finished since they were loading it yet Wesker doesn't deploy it for another 9 months despite nothing stopping him. There was something else I remember thinking about too, something to do with timing of plaga 2 release and conflicts between a file and Adams blog, I've not thought about this since near RE5s release so the details sketchy.

Outbreak is just magic, the story is a complete mess if you can call it one. The scenarios just aren't linked well at all and are more like individual tales and this was the game that completely changed the scope of Raccoon City adding things that just do not fit, a city of 100,000 is not enough to keep a zoo running, is hard to sell a tram system yet alone a tram and a underground trainline. It makes it own alterations to existing layout also, something ORC get criticised heavily for though I suppose Outbreak was not anywhere near as drastic. Of course the already mentioned missiles, not sure that computer controlled Tyrant really fits in with what Umbrella Chronicles was going for.

Speaking of UC, and Tyrants in general. We're led to believe the T-002 was the best in the biz, then we find there are more and better Tyrants (T-103) that were created based on the T-002 after the Arkley combat data was obtained according to Archive 1, Survivor and Weskers Report II tells us they super hard to make and needs kids scared brain chems or whatever it was, then UC gives us Ivans, modified T-103s that were about even before RE0, made from clones was it. So Ivan (that existed before the T-002 combat data was obtained) is a modified T-103, and T-103s were created after the combat data was obtained. Plus Tyrants are really hard to make due to rare chemistry needed, but can get the stuff from scared kids brains, but then already just cloned someone and made them anyway. TALOS can just go to hell.

Revelations has plenty of plot holes, as from those mentioned already Jessica's motivations for shooting Reymond not once but twice doesn't make sense given the final twist of the story. Whats his face living on a ship for a year, underwater no less not to mention his injection of the virus not having immediate effects have little to poor explanations.

Was it ever explained how Claire knew Wesker in CVX?

There are lots of things, as said these are just off top of my head. I've noticed loads over the years, some eventually got answered.

Q15) Were you or FLAGSHIP aware of the story inconsistencies in "Wesker's Report" written by Mr. Hiroki Katoh? Such as Leon joining an underground anti-Umbrella organization and Sherry being captured by Wesker, which contradicted the Epilogue Files you wrote?

*laughs*

Mr. Katoh wrote Wesker's Report around the same time that BIOHAZARD 3 was being developed, so there may be some inconsistencies between his work and the world that I created.

So the mystery that is Revelations is still not complete. =P

"MYSTERIOUS JOURNAL"
He's finally made his move. I don't even know how long I've been waiting for this.
My mission is the key to the success. It's the reason why I've given up so much already.
In order to get incontrovertible evidence to use against Morgan, I had to bring Veltro back to life.
I thought this plan was weak - dangerous even - when O'Brian first brought it to me, but we couldn't figure out any alternative that would work.
We set up a fake base of operations for Veltro in the mountains of northern Europe, and then we spread rumors of a big op Veltro was planning to the BSAA.
When the BSAA began their investigation, Morgan started to panic. Those spies of his must have tipped him off.
Morgan is very careful and he's suspicious by nature. I suspect that everything went well because we didn't leak the news of Veltro directly to the FBC.
It's like the saying goes: be careful of the web you weave. I was able to hijack the Queen Zenobia before Veltro could do anything to it. Even still, I could not find anything to link Morgan to his illegal activities. As such, it has come time to become more proactive in this mission.
I must bring the BSAA agents here, and then disguise myself in order to deceive them into thinking that Veltro has managed to survive.
Any of Morgan's spies in the BSAA will try to contact him, and that's when we'll get our chance.
According to O'Brian's report, Morgan's dogs already attacked the fake base we set up.
The parameters of this mission are quite fluid, and, as such, leave lethal options in the table.
I will do whatever it takes to see this mission through, even if it costs me my life.

(IT LOOKS LIKE A PIECE OF A MANIFESTO.)
Destiny, and I do not mean to sound flippant, is made before we even get a say, and is the will of a higher power.
The impure will not be cursed; it is their destiny to be torn apart by the fangs of the hounds.
I cannot spare sympathy for the victims of this world: they are the ones who created it. It is the same world that robbed this dog of its bite.
No longer will I howl; I will sharpen my fangs. No longer will I roar; I will sharpen my claws. All our comrades are waiting for the time when they may sacrifice themselves to the cause. Only the hounds are pure of purpose, and it is only they who may purge the world.
We do not hunt alone. We hunt in packs. We are Veltro.
Earl Brinvico

There are only really two points of Revelations we are yet to fully understand.

1. How and when was Jack Norman's threat to the BSAA sent? If it was a re-record from the Terragrigia Panic then surely everyone would know about it.
2. Who started the deliberate flooding in the bilge? It could only have been Raymond and yet he did not want to harm Parker and Jill.

1. I think this thrat was sent to BSAA right after Terragrigia panic, but O'brian hold it and release it just when he need it.

2. Malufaction problem perhaps?