I have a Squier affinity j bass V that I bought about 9 months ago. It was working great but the last couple days for some reason when I play there hear a low fifth playing under the note.
That's basically a subpartial. Try damping all other strings. Does it persist? If not, it would be sympathetic vibration. If it's stronger than it should be, it could point to a loose bridge or nut coupling the strings stronger than expected. Of course, detuning either string just a bit should also help.
If it's not that, there is the possibility of (again) bridge or nut not providing a good fixture for the string, triggering an additional string reaction with a delay (if the string gets an additional sideways jerk at maximum string displacement, this will add something like a fifth). If pressing down the string with something hard but not damaging (piece of plastic or wood) into the groove of either nut or bridge should make a difference then.
Another possibility is that your amplifier or speaker or some stompbox adds this fifth as an unintended side effect, so you should try setting your amp chain up to be as clean as possible and see if the effect persists.
Also if you have an opportunity to record straight from the instrument plug, it's an idea to listen with headphone or similar and see whether the effect persists.
And maybe you are just hearing things: the sense of hearing can reconstruct fundamentals even when it only hears the partials. This is used as an organ trick, using both 8" and 5⅓" pipes to create the illusion of a 16" pipe one octave lower than the actually played note from the 8" pipe.