Update on mine:
Skoda dealer have been terrible, from start to finish. They 'checked' my gearbox 4 times and said it had no issues. I personally took it to them as was able to replicate the issue with the 3rd gear within a minute. It's now been in the garage for two weeks and they're replacing the entire gearbox, not that they would tell me what they found was wrong with it. For those looking at this looking to purchase:
* repeatedly depress the clutch, put it into 3rd gear and out, then back into neutral. Depress clutch and repeat. If your 6 speed manual has this problem this is how to replicate it and it will either grind OR become increasingly difficult / impossible to go into gear. It is something to do with the depression of the clutch and then moving it into the gear that it doesn't work correctly.