We did look at all the episodes, and didn't see any problems at the end of 2 and beginning of 3 (we are in the US), but we did find that the whole ending of the series is missing, and it's available for free on Syfy and Amazon:
Haven on Netflix (missing episodes)
Seasons 1-4: All episodes listed correctly in the US
Season 5: Episodes 1-13 on Netflix, Episodes 14-26 free on SyFy
UPDATE: Thanks Danielle for the fix, SyFy now only has episodes 23-26 of Season 5 for free, and 1-13 are on Netflix. So the only way to get Episodes 14-22 would be to buy them on Amazon for $1.99 each... happy pirating!
If you like Haven, check out the great show Falling Skies free with Prime on Amazon.