As
FunkyMonk has remarked, the format of your input file (primarily space-separated) doesn't match the way you split each line into fields (split on ";"), so it is not surprising that some of the fields come out undefined.
Moreover, you say:
Here is my output file
DAL11 527 530 3
ACA87 531 533 2
SHT8K 528 535 7
DLH9F 533 537 4
...but the typical print statement in your program is
print OUTFILE "$aircraft_id;$ATO_min;$CTO_min $delay_ATO_CTO_m";
That would print a semicolon-separated output, not the space-separated one you present. You need to reconcile your separators.
Anno