The Mallards suffered their first defeat in six games and will be disappointed not to have made more of this match.
Harry McConkey's men started brightly with Hume drawing a save from Anderson and McCartney seeing his deep cross headed off the line.
The home side also created a few half chances before taking the lead on the half hour; Matthew Ferguson rising highest in the box to head in Scott Davisons cross from the right.
On 37 minutes the Mallards scored a deserved equaliser. Ryan Campbell shot from distance which Anderson parried and Nathan Cashel reacted quickest to prod in from 6 yards for his fourth goal in four games.
On the stroke of half time John Connolly produced a super save with his feet to deny Ryan Deans, having got across his goal line quickly.
The second half was a quieter affair with things not quite clicking for the Fermanagh side. Connolly again came to the rescue, showing great bravery to save on the goal line with 3 players sliding it to try and get on the end on a teasing cross.
On 76 minutes Ferguson netted his second, showing physical strength down the left before cutting in on his right foot and finding the bottom corner.
Robbie Hume worked himself into a couple of good positions to shoot but couldn't find the target as the Mallards struggled to find a way to goal and became frustrated with their play.
Indeed Connolly produced another top class save with his fingertips to prevent Ferguson from notching up his hat trick.
Not the result that the Blues wanted but this is only a minor set back in Harry's overall plan.