There could be some small level of inaccuracy due to local procedures.
For example, UK FMP positions have an agreement to vary the window by +/- 5 minutes if the aircraft is operating domestically and subject to a UK slot. This isn't co-ordinated with Brussels, so could show as a violation on their system even although it has been approved locally by the agencies involved. Other countries or ATS partnerships may have similar things in place.
There could also be some variance with timings, depending on how the CFMU calculates rounding up/down times. The UK rounds down if it is minute +29 seconds or less, and up if it is minute +30 seconds or more. Let's give you a CTOT of 1200. So if you get airborne at the end of your slot window of 1210 at 1210.29, then the UK will deem you departed at 1210. But it may be that the Brussels system says that is after 1210 and so you have violated because you departed at 1211 in their system. The opposite could also be true for an early departure, with the UK assuming you have taken off in the next minute (i.e. within the slot) at 1154.30 (UK time thus 1155) but Brussels deem you have gone a minute early as it is still 1154 to them. I don't have that detail of knowledge of the CFMU system, but it is a possibility.
Other than that, it seems to be down to the departure airfield for allowing the non compliance. Heathrow, for one reason or another, is usually top of the pops in the UK each day
