Some can be explained away quite easily, others with difficulty, and some not at all. Anything involving ST: Eleven ... well
For example: Relics - Scotty has transporter-induced, mild amnesia (spending decades in an atomized limbo cannot be healthy). The naked time - Scotty DID start the engines in a LOT less than 30 minutes; The jem'hadar wear clothing/armor that renders a diluted wide field phaser useless; etc.
Some of these are old and well known continuity problems. Scotty thinking Kirk was alive in Relics and its infamous rationalization even had a joke made about it on Family Guy. The bit where the turbolift journey in The Enterprise Indicent was timed was hilarious, and I also got a laugh out of Trip being too cool for the laws of physics.
The last one with the deleted ST09 scene- easy. It was on a different part of the planet plus that factory/refinery in the background may have heated up things in the immediate area.
This. Nicely done and much more fun seeing those old chestnuts done visually rather than in dry print.