Nope, no cease fire orders, but in a new game the same is just happening to me and maybe those details might help narrow down the issue:
My CTF is protected by 2 flights of 10 gauss-fighters (higher ini, distance = 0 - they have been following the CTF for about 1 hour now) while 2 scouts and my bombers are trying to run down a couple of enemy missile carriers. Those have already fired their missiles at the CTF (size4, speed just at 18k) and my fighters have completely destroyed 4 flights of 2x14 missiles already, but on the 5th flight suddenly 4 fighters (007, 008, 009 and 010) did not fire and 2 missiles got through. Nothing has changed since the first missiles were shot down and the other 6 fighters in the flight did fire as ordered.
Out of curiousitly I took a look at the inidividual fighters initiatives (despite all of them being in the same flight), the flight is at 113 ini (highest officer has fairly low ini, will have to change that once we get back to Earth), while 007's C. O. has 183, 008 = 193, 009 = 127, 010 = 112. So even if individual initiative would be taken into accout (which it is not AFAIK) the only fighter which might have had any reason not to fire would have been 010. And vs. the previous missiles at least fighters 007 and 008 did fire (destroying the last missile).
What is interesting is that 011-020 and then 001-006 fired correctly (and in this order), it looks like the last 4 fighters were essentially forgotten or maybe that the game considered those last 2 missiles to have been destroyed after fighter 006 fired at them.
Hmm, I just counted the missiles acutally destroyed by the 16 fighters that did shoot and came up at 23, but with fairly slow missiles like these (18k) some misses vs. a target moving at 3k should be normal I think. But on the other hand - even if this seems fairly unlikely - maybe those 4 fighters did shoot, destroyed 3 more missiles and 2 made it through in the end, but this just was not displayed in the event log?