Move the Fighter into a hangar (Carrier, PDC) and try again. It should then Carriers MSP then for repairs.
I have designed a PDC with an Hangar:
NORAD IV class Fighter Base 64650 tons 1275 Crew 6246.3999 BP TCS 1293 TH 0 EM 0
Armour 5-143 Shields 0-0 Sensors 16/16/0/0 Damage Control 10 PPV 352.8
Annual Failure Rate: 22645% IFR: 314.5% Maintenance Supplies 0 SP
Parasite Capacity 15000 tons Magazine 3850 Flight Crew Berths 9
Maintenance Modules: 2 module(s) capable of supporting ships of 400 tons
Fuel Capacity 2 000 000 Litres Range 0.0 billion km (0 days at full power)
Twin Heckler & Koch Gauss Cannon R2-100 Turret (20x4) Range 20 000km TS: 4000 km/s Power 0-0 RM 2 ROF 5 1 1 0 0 0 0 0 0 0 0
Fire Control S00.5 24-3000 H70 (2) Max Range: 48 000 km TS: 3000 km/s 79 58 38 17 0 0 0 0 0 0
S-6 Missile Launcher (15) Missile Size 6 Rate of Fire 60
Pedley Systems Penguin Missile Fire Control FC111-R60 (3) Range 111.5m km Resolution 60
ASM-1 S-6 "Penguin" (104) Speed: 18 000 km/s End: 107.7m Range: 116.4m km WH: 8 Size: 6 TH: 96 / 57 / 28
Runion Electronic Systems Thermal Sensor TH2-16 (1) Sensitivity 16 Detect Signature 1000: 16m km
Pedley Systems Active Search Sensor MR118-R60 (1) GPS 11520 Range 119.0m km Resolution 60
Pedley Systems Missile Active Search Sensor MR0-R1 (1) GPS 9.60000038146973 Range 760.0k km Resolution 1
Runion Electronic Systems EM Detection Sensor EM2-16 (1) Sensitivity 16 Detect Strength 1000: 16m km
Missile to hit chances are vs targets moving at 3000 km/s, 5000 km/s and 10,000 km/s
This ship is classed as a Planetary Defence Centre
It has Damage Control, Maintenance Modules, Maintenance Storage Bays a huge hangar.. but when I land the fighters there (as mothership) and I try to repair the systems, the game always send the message that there are not enough maintenance supplies for the reparation.