As the title says, the D&D group I DM for has a Flind boss coming up, but I am wondering if it was too cruel to set up.

The party is four level 5's, with two level 4 sidekicks. They have killed so far:
1 Firefist + 1 Eater of Hope
1 Yuan-ti Malison + 12 various undead
1 Mindwitness + 1 Yuan-ti Nightmare Speaker + 15 Yuan-ti Purebloods (Dungeon run, so not all at once)
1 Shadow Horror + Shadowghast/Shadow Demon Adds
1 Couatl + 1 Battleforce Angel
2 Invisible Stalkers

Now their village is being assaulted by an army of gnolls. In game time they have spent 4 hours hunting gnoll assassins and clearing hunting parties when they can, and are quickly approaching the Gnoll Flind that is leading the Raid. They have handled a lot of things so far, with only 3 deaths (Death by Stalkers, Shadowghast/Shadow Demon combo, and unlucky guy getting critted 7 times by Yuan-ti Purebloods.) but the Flind absolutely has the ability to OHKO any of them, even the Barbarian. 
Have I made a mistake by setting up this encounter? The CR calculator labeled it at "Medium Difficulty" but I am unsure.

Vince is right. An out-of-the box Flind will be owned in 2-3 rounds max by the party. Frankly I'd be shocked if a normal Flind made it to round 3 against 6 level 4-5 characters. The only way this would not be true is if it's the 3rd or 4th encounter without a rest and they are low on spell slots and special abilities and have lost some hp. But if they go in fully rested, it has no chance.

The thing has +0 to initiative, which means that odds are, 2 or 3 PCs and at least 1 SK will go before the Flind can even move. Someone will hit him with something like Hold Person and that could be the end of the battle. The Flind will be lucky to K-O a single character before he's dead.

if you want it to be a tough fight make him a named Legendary boss. Give him 1 (not 3) use of Legendary Resistance, just to prevent a hold-person save-or-suck battle-ender from hitting on the first round. Give him 2 legendary actions per round... one some sort of move ability that avoids attacks of opportunity (call it "slip away" or something), and one a single-shot use of the flail. This can be done at the end of each PC's turn, so even if the Flind tanks his initiative roll, he can do SOMETHING to them earlier in the round. Plus at that level, if they have not seen a Legendary foe before, it will absolutely freak the players out (it did with my players at level 4 the first time they fought a legendary boss, also coincidentally a Yuan-Ti).

You may need to compensate by slightly altering AC or HP (but probably not)... Say, dropping AC to 15 and hp to 110 or so. I'd rather do that and give it some Legendary juice, rather than leave it at 16/127 and watch it die without even getting to go.