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My suspicion would be that you had selected a different ship and that one got the upgrades.
To upgrade the ship you fly yourself, dock at the warf and use the "upgrade/repair ship" button in the docking options window that opens once you dock. There it opens the upgrade screen and the things are installed after you hit confirm order (assuming there are enough wares on the station).
MFG
Ketraar
MFG
Ketraar
Argon Prime and TS7 are your best bet for (S & M sized) instant ship upgrades.