There are flight numbers with 1, 2, or 3-digit numbers (<1000) and there may be sCO/sUA issues in numbering, but also the whole range up to 9999 is not available. Express carriers get certain ranges each. Charters have a range. Codeshares have ranges by carrier. The actual number of flight numbers available for UA/CO metal isn't as large as it may seem. (This does not preclude on-time data shenanigans being possible, of course.)
Per the current UA timetable:
Flight Number Ranges
1 - 1299 United Airlines
1340 - 1344 ExpressJet-Extra Section
1400 - 1764 United Airlines
2050 - 2119 UA Extra Sections - (XP)
2193 - 2200 Cargo Extra Section (XF)
2900 - 2949 Cape Air (Carribean)
2950 - 3049 Great Lakes Codeshare
3050 - 3149 Silver Airways Codeshare
3150 - 3249 Amtrak
3250 - 3254 Commutair Extra Section
3255 - 3274 UAX - ExpressJet - CO Contract
3275 - 3294 Skywest Extra Sections
3325 - 3329 Trans States Extra Sections
3330 - 3434 UAX-Trans States
3435 - 3439 Shuttle America Extra Sections
3440 - 3584 UAX-Shuttle America
3585 - 3590 UAX-CommutAir DH3 - CO Contract
3591 - 3604 UAX-CommutAir DH2 - CO Contract
3605 - 3714 UAX-Go Jet
3715 - 3717 Go Jet Extra Sections
3720 - 3724 Mesa Extra Sections
3725 - 3804 UAX-Mesa
3805 - 3854 UAX-Expressjet
3855 - 3904 UAX-Republic - UA Contract
3905 - 3919 UAX-Shuttle America
3920 - 3965 UAX-ExpressJet - CO Contract
3966 - 3969 Shuttle America Extra Sections
3970 - 3973 Silver Airways - Extra Sections
4051 - 4066 UAX- Silver Airways - IAD
4067 - 4084 UAX - Silver Airways - CLE
4085 - 4769 UAX - ExpressJet - CO Contract
4770 - 4834 UAX-CommutAir DH2 - CO Contract
4835 - 4859 UAX-CommutAir DH3 - CO Contract
4860 - 4868 UAX-ExpressJet - CO Contract
4869 - 4947 UAX-Republic - UA Contract
4953 - 4955 UAX-Republic - Extra Sections
4965 - 4999 UAX-Skywest
5000 - 5021 UAX-CommutAir DH2 - CO Contract
5022 - 5037 UAX- Trans States
5038 - 5082 UAX - Cape Air GUM
5083 - 5083 UAX Cape Air - Extra Section
5090 - 5122 UAX-Mesa
5123 - 5155 UAX-Shuttle America
5156 - 5269 UAX-Skywest
5270 - 5289 UAX- Trans States
5290 - 5659 UAX-Skywest
5660 - 5684 UAX - ExpressJet - CO Contract
5685 - 5774 UAX-ExpressJet - former ASA
5775 - 5778 ExpressJet - former ASA Extra Sections
5779 - 5809 UAX-ExpressJet - CO Contract
5810 - 5899 UAX-Expressjet
5900 - 6189 UAX-ExpressJet - CO Contract
6190 - 6539 UAX- Skywest Airlines
6540 - 6544 UAX - Bus Service - EWR-ABE
6545 - 6548 UAX - Bus Service - IAH-BPT
6549 - 6598 Aeromar
6629 - 6748 AVIANCA
6749 - 6828 Air New Zealand
6829 - 6848 LOT-Polish Airlines
6974 - 7073 SAS - Scandinavian Airlines
7074 - 7173 Copa Airlines
7224 - 7253 South African Airways
7254 - 7283 Croatia Airlines
7284 - 7323 Asiana
7424 - 7623 Air China
7624 - 7668 Aer Lingus
7669 - 7768 Swiss
7769 - 7792 Turkish Airlines
7793 - 7878 Hawaiian Airlines
7879 - 7914 IslandAir
8015 - 8714 Air Canada
8715 - 9589 Lufthansa Airlines
9590 - 9639 TAP-Air Portugal
9640 - 9739 ANA-All Nippon
9815 - 9854 Austrian Codeshare
9855 - 9868 Egypt Air
9883 - 9899 EVA Air
9900 - 9998 Brussels Airlines