Same with Jurassic park 3 and the T-Rex that somehow managed to kill everyone while at the same time being still confined in the cargo bay.
The original script made perfect sense and then for some baffling reason they deleted important scenes for the theatrical release. In the original script the raptors were also in there, they got out through the small hole the T-Rex made, and then they killed everyone and jumped into the sea and swim to shore. Then for some totally bonkers reason they edited it and decided that the raptors had already been transported earlier and had nothing to do with this bit.
Which would have been fine but then they should have reshot the entire boat sequence. The problem is then they would have needed the T-Rex to have escaped. Not really sure why they didn't do that as it didn't really change the plot all that much and at least then it would have made sense.
I think the problem was that they decided late on in production that they didn't actually want to deal with the CGI of having the raptor swim in water since water is hard to do. But again they should have reshot it.