Not being there and not seeing any attached example images, consider a few things:

1, as User ID notes, you should have no focus actions related to the shutter button. With the BBF assigned to a rear button on the body, nothing related to 'focus' should occur with the shutter release button.

2, Check the focus limiter switch on the lens. If your subject is too close and the limiter switch is set to a longer distance, that would explain being unable to focus on a closer subject.

3, Confirm your BBF usage. In addition to having no focus actions on the shutter release button, you need to engage focus with your thumb, holding down the assigned BBF button with your thumb. So the process would by:

i, Raise the camera to your eye.
ii, Press and hold the BBF.
iii, Track the subject (moving) or the static subject, both situations using AI Servo
iv, Release the shutter with your index finger while still holding / pressing the BBF.
v, Remove your index finger from the shutter, when you're done capturing images, either a single frame or short burst.
vi, Release your thumb from the BBF when there is no need to focus on the subject.

4, If applicable, review your touch screen settings and assure your face isn't accidently repositioning the AF location when your have your camera raised in a shooting position.

5, Check your AI Servo settings and see if you linked the AF location to the camera orientation, horizontal vs vertical. See page 565 of the EOS 90D Advanced User Guide.

6, Re-read the AF Settings in the Advanced User Guide, starting on page 123, especially the settings related to the Initial AI Servo AF position and Face+Tracking, Continuous AF, AF-assist beam, and Eye Detection AF.

7, Review your Tracking Sensitivity settings, starting on page 559 of the Advanced User Guide. I prefer customized settings for 'locked' tracking and 'responsiveness'. Read these settings and consider making the camera more likely to remained 'locked' (-1) and more responsive (+1). Consider too making the camera responsive to sudden movements, page 560, with +1 for Acceleration. Finally, encourage the camera to switch points with +1 on the AF switching.