I had the very same issue (green footprint icon was displayed, but no yellow animal indicators on companss and map) and I finally managed to fix it myself.
Since I was preparing to send in a formal bug report, I am including the already gathered details at the end.
Luckily, I just encountered the problem in-game (spotted a rabbit, crouched, but no animal marker showed up), so I left the game and had a reproducible situation to test with.
What I actually did until the problem was solved, was:
Validated game files via Steam (recovered one corrupt file - but the problem still occurred, when I continued the saved game) Rebooted Windows via Start->Restart (not just shutdown and switch on again, since this is not really restarting Windows) After that reboot, I immediately continued the game and the yellow icons were there again!
So hopefully this helps any others to get back their icons.
Here is the bug information - might also help someone:
Summary: animal tracking doesn't show icons anymore
Game Version: A18.4 b4
OS/Version: Windows 10 Pro V1909
CPU Model: Intel i7 3770K
System Memory: 16 GB
GPU Model and VRAM: AMD RX570 8 GB
Screen Resolution: 2560x1440
Video Settings: Medium - no custom settings
Game mode: SP
Did you wipe old saves? No
Did you start a new game? No - this occurred in the course of my very first game
Did you validate your files? No
Are you using any mods? No
EAC on or off? according to log: GamePref.EACEnabled = False (but I never switched it off)
I'm on AnimalTracker Skill Lvl 2 and at first the tracking skill worked as intended, but now it is broken in the following way:
When I crouch and animals are nearby, the green track symbol appears in the lower left with the "20 sec" label.
However, neither on the compass nor on the map any icons for the animal are displayed.
This problem is permanent, i.e. it happens even after reboot or restart of the game.
Detailed steps to reproduce the bug:
1) Go near animal
2) Crouch & wait until green footprint-icon appears
3) Look around and check compass - it doesn't show a symbol
4) Open the map - it also doesn't show an animal symbol
Actual result: No animal icons shown
Expected result: The compass and the map should show the direction/position of the animal with a yellow animal icon