If you are using altirra check your overscan setting.
I don't recall seeing the glitch over to the right of the screen (I may have just not noticed) but I've definitely seen the phantom objects at the top of the screen. I was using Atari800Win+ FWIW.
the upper screen issues show even on real ntsc hardware and 1084 monitor output...
The "glitch" on the right side of the screen is standard ATARI behavior whenever wide screen is enabled.
The "Glitch" are disabled sprites and normally should not be visible on standard NTSC TV Sets. It is difficult to know what happens with certain monitors This was tested on real hardware. Widescreen shows some artifacts in emulation if overscan is enabled. Not sure if there is a vertical adjustment on a 1084 monitor.