Squeaky noise  

Lubrication

Have you tried to lubricate your beraings?

Re:Lubrication

I applied a small amount of grease to the smooth rods, right before the print that it's printing in the video. Might need to apply more. I don't seem to be able to replicate the sound when I move the y-axis by hand

Can't lubricate bearings by greasing rods

That won't work.  Remove the rods.  Repack the bearings.  If there are scratches on the rods, order new rods and bearings and grease.

bearings

This will only work if you lubricated the bearings at the start (when assembling).  I do this once a month for mainternace, but when I chnage bearings or assemble a printer, I packed my bearings as Dan said above.  

Posted by: @henrikbiscuit

I applied a small amount of grease to the smooth rods, right before the print that it's printing in the video. Might need to apply more. I don't seem to be able to replicate the sound when I move the y-axis by hand

Re:Can't lubricate bearings by greasing rods

Is there a good guide on how to do this? Like how to disassemble the y-carriage, and applying grease to the bearings.

I have this thing called "Spider grease", which is pretty thick and grey (kinda like thermal paste for a CPU). Will this work on the bearings? It's a PTFE silicon grease.

It said in the manual that the bearings was greased. I have been using it for about 326 hours (13 days and 14 hours).

No sticky goo. Use a white lithium grease

Y is the easiest axis to service.  Take the bed off.  All the way.  Place it behind the printer and try not to torque the wires bundle.  Now remove the Y rod holder clips (cut the zip tie if MK3s, unscrew and prepare to remove rod for MK3S+).  Remove the Y rods.  The bearings should now be riding on the rod with nothing else attached to them.  Slide the bearings off of the rod, careful in a horizontal position may be best so you don't jiggle any loose balls and lose them.  

Take the greasing tool that came with the kit.  Screw it onto the grease tube (that came with the kit).  One tube will service one set of bearings - assuming you are using the small prusa grease tube.  Align the holes in the greaser with the  balls in your linear bearing, and insert the greaser fully into the linear bearing.  Now squeeze the tube and hold the pressure - I would recommend doing this over a paper towel as the grease will push the packing oil out of the bearing and it will drip as you grease the bearing.  Repeat for all bearings.  

Now re-assemble the Y rods - put the bearings back on (two on one side, one on the other - exactly reverse of disassembly).  Re-assemble the Y carriage per the instructions in the book - following all of the steps so that the rods and bearings end up aligned.  Put the bed undercarriage onto the Y rods, and start slowly tightening the clips.  You do not want to deform the shell of the bearings at all.  If you over-tighten this step, you will have calibration woes later on.  Reinstall the heat bed (spacer game).

For the X axis, you will want to first remove the Extruder body from the Extruder carriage - the screws on the back of the extruder carriage are most of this.  You don't have to remove the extruder - but you'll have to remove the Z rods to free up the X carriage.  X belt, X motor ... the works.  You will want to grease the three linear bearings on the X carriage (x rods, two on top rod, one on bottom rod).  You'll want to also grease your Z rod bearings if you never have done that.

It's a job to take your time with, work with the online assembly manual - and get used to tearing her down if you plan on continuing with linear bearings that have balls in them.  I only use them on the Z rods myself.