So I'm just looking at some numbers for the Governor's race. Bridgeport is 60% in with a total of 25,650 votes cast (everyone else is 100% in). There is a 75%/25% split in Malloy's favor so far.
25650/.60 = 42750 votes @ 100%

If the split remains, which is likely, we end up like this:
Malloy:
42750*.75 = 32062.5 (Rounding up for Malloy BP is a Dem stronghold) - 19148 (BP votes already in for Malloy) = + 12,915
Foley:
42750*.25 = 10687.5 (Rounding the half vote down for Foley) - 6502 (BP votes already cast for Foley) = +4,185

This would make the totals look like this:

Foley with 25% of Bridgeport  =  556,291
Malloy with 75% of Bridgeport =  556,597

If Malloy remains consistant, he wins. If he dips below 75% by one half of a percentage point, the race goes to Foley.

Let me point out that if there was anything not above board, Dan Malloy had nothing to do with it - I have never met a nicer, more upstanding person.

So here is my cynical take: either there was complete incompetence or the ballots were purposely under ordered. If they were purposely under ordered it was either in hopes that a crisis turns people out or in a close race, you mount a chall...enge based on x number of voters unable to cast their ballot. It's too easy to blame the Republicans and they would make a believeable villian if they held any power in Bridgeport...but Bridgeport is a Democratic stronghold. Not only that, but the Secretary of State informed them before election day that needed at least as many ballots as they had registered voters. That information apparently was ignored.

When trying to figure out what happened, you have to look at who would have the most to gain/lose. I'm left with only the Dems. The Republicans taking Bridgeport is completely unbelieveable, either every registered Democrat in Bridgeport would have to fail to vote or half would have to vote Red for it to happen. The ballot shortage and subsequent reporting of it on election day does present a crisis that would motivate an electorate that may otherwise be ambivalent - afterall, the Dems will win Bridgeport, the only question is, how big the margin will be.