The front brake rotors can warp and cause a vibration when braking. The rotors will need to be machined or in cases where they are worn to thin, replaced to correct this issue.
Car problem reports
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Most reported 2006 Honda Pilot problems
On certain models a leaking side marker light wire harness can cause a water leak inside the vehicle. Resealing the wire harness where it goes through the body into the cabin area should stop the leak.
An overheated wire in the head light harness can cause the low beams not to work. Replacing combination light/turn signal switch switch, the wire for the low beams, and the combination switch connector (if damaged) should repair this issue.
Noise and judder can develop from the rear axle due to differential fluid breakdown. Replacing the fluid will commonly correct this issue.
Map light will not turn on when opening drivers or passengers door. Caused by a faulty door switch. Requires replacement of door switch on side of non operation.
A knock or clunk type noise may be noted from the front suspension over bumps. This is can caused by worm stabilizer (sway) bar links. Replacing both stabilizer bar links will commonly repair this issue.
A chirp noise from the timing belt area can be caused by a tilted idler pulley. Installing a corrective shim from Honda will commonly correct this issue.
On certain models the PCM misinterprets data from the coolant sensor and sets a false Check Engine light (MIL). A software update from Honda will repair this issue.