While I was calibrating my flow rate/extrusion multiplier, I noticed that one layer is shifted slightly. I wanted to re-print the cube in-case it was a fluke, but after two more prints, I saw that the same layer was being shifted in the same way. Also, that is the only layer that is shifted, every other layer is perfect/almost perfect.
I'm using Cura 4.3.0, on an Ender 3 which I purchased about a month ago. The extruder is upgraded to a Trianglelabs Bondtech BMG clone. The E, X, Y, and Z steps have all been calibrated. The bed is level (I'm using a Creality ultrabase glass bed). I have upgraded the stock PTFE tubing to Capricorn, upgraded the PTFE coupler fittings (they have plastic tab inserts to keep the tube in place). The X gantry is level. I've also re-lubed the z-rod with super lube, made sure the lead screw nut is loose and printed out a z-spacer for the z stepper motor. That's about it, I'm still using the stock board but my SKR mini is in transit right now. Finally, the filament I'm using is the filament that Creality bundled in with the printer when I purchased it off their official website so I don't know how quality their filament is.