Below is a complete list for the locations of all minikits in Chapter 03: Rail Hydra.
Part A MInikits
Minikit #01: You need someone who has access to the telekinesis ability to put the basketball through the hoop.
Minikit #02: Activate the S.H.I.E.L.D. control panel using a Hydra agent to get a floor buffer from the right room. Move this device over a total of five dirt piles around the area.
Minikit #03: This piece requires you to destroy a total of five Captain America posters around the gym. There are a couple tacked on the wall to the rear of the boxing ring; one on each wall to the left as well as to the far right; the last one is behind the green lockers.
Part B MInikits
Minikit #04: This piece can be seen hovering over the switch on top of the elevator. Fly over there to claim it.
Minikit #05: There's a gold crate located to the right of the Collector's position that you can destroy, then rebuild into a speed pad.
Minikit #06: To get this minikit, you have to clear away some of the containers on the right side of the control room. Build handholds from the new bricks to reach a walkway above you.
Minikit #07: You need someone with stealth capabilities to slip past the cameras undetected and grab this collectible in the back.
Part C MInikits
Minikit #08: At the start of this section, turn around and make your way down along the rear of the train to find this minikit.
Minikit #09: This minikit is found just past the second group of electric pylons, wherein you must use lasers to cut through some gold objects. Build a glider from the pieces then get on it.
Minikit #10: Use someone with scanner to check the section just below the red handle to find a target marker that you can shoot at to get this collectible.