The online check in system doesn't deliberatly allocate seats seperately, it purely fills the aircraft up from the back section (not rows 25/26 on a 733 or 41/42 on a 757 due to these being classes as exit rows) So say all of row 40 was full, all of row 39 was free then they system would allcoate 39ABCDEF to a group of six, however say there were a group of five travelling it would allocate 39ABCDE then the next two would be allocated 39F & 38A. However say the following two rows had already been pre-booked then the system would just move onto the next free seats, thus meaning people can get split up.
There is no trickery behind it, its not a money grabbing exercise as once you have checked in online you cannot pay to move your seats, and we do not charge at the airport to re-seat passengers. There is really no other way of doing it, it really is no diffrent to how we allocate seats at check in, but obviously we use common sense to balance the aircraft and to put children with parents. Most likely the reason why this happened for you, if you book a child as an adult on the booking engine it will not pick up that the child is infact a child. If the child is booked as a child (allocated M-Male, F-Female & C-Child) then the entire group would be allocated seats together as the system recongises this. The vast majority of people do not book children as 'C' they simply put in say 2 adults instead of 1M/F & 1C. This makes it difficult to then allocate seats as from the computers point of view (and check in staff's point of view) this 'adult' is able to be sat away from their parent/sat on an exit row etc) This complicates things when they turn up to check in demanding to be sat together and that Jet2 has deliberatly sepetated a 3 year old child from its mother and going on with the usual ... "you are the worst airline in the world" etc ... But hey its a no win situation for Jet2 or any airline, its a million times easier to apologise and do your best to reseat the passengers instead of explaining that the error was in their hands.
Whats all this about check in staff not letting seats be changed?! You are correct that it is Jet2.com policy to not seat children seperate from adults, and the upmost is done by check in staff to avoid this, and should this occur we will make seat changes to peole who have already checked in and on boarding the aircraft they will be given new boarding passes. People may be unaware of the practices used at check in, but basically we go through flights before hand, any large groups, parents with infants/children and wheelchairs are allcated seats together, followed by groups under the same booking reference and lastly followed by single travelling passengers. So basically on a busy flight the seats are pre allocated to everyone before they turn up to check in as this means that people are guaranteed to be sat together (As far as it is possible) - there are always some cases where is it not possible.
At the end of the day there is always someone complaining at check in that they are not sat together - simple answer to this - pay the measley £3.99 fee to guarantee you are sat together or come to check in as early as possible and we can un-allocate seats and then re-allocate them to accomoate your request.