Ender 3 Y-Axis Stretched (I don't believe it's layer shifting)
If an axis doesn't print the sizes you command it there are basically 2 options causing this.


The printer is incorrectly configured,
The printer has an hardware issue.


To find out which of the 2 is applicable, you need to look into your setup and into the firmware settings. E.g. from the printers display you can read the amount of steps the stepper needs to make to move the axis 1&nbsp;mm. Alternatively, send M92 through a terminal and look at the steps per mm. If X and Y are the same, the firmware is correctly configured and you are facing a hardware issue. Note that for the stock Ender 3 the value for X and Y needs to be 80&nbsp;steps/mm. Do not alter these values!!! These values are based on the mechanical layout and the micro-stepping used by the stepper drivers.

Since you have flashed a stock hex firmware file it is highly improbable that the firmware contains the incorrect steps per mm value for the Y axis (unless you accidentally changed this through the interface/display). This leaves you with a hardware issue. Common reasons that could identify the source of the problem are:


Loose grub screw of the pulley on the stepper,
Missing steps, e.g. due to too much friction (if dimensions are smaller, in your case this is not the problem, it is added for completeness),
Loose, under tensioned belts,
Stretched belts as a result of over tensioning the belts.


Considering the stretched Y dimensions, the most logical explanation would be that your belts are stretched, you cannot fix this by changing the steps/mm value, it requires mechanical attention; i.e. replacing for new belts.