A lot of "exposed bonded die" packages caution against using ultrasonic cleaning.

This is especially true for TCXOs, which also have the entire loose crystal in them on top of the controller die, and for MEMS mics, which are designed to be sensitive to vibration. But it's also true for things like common CMOS image sensors, which are "exposed die", but not mechanically sensitive otherwise.

Bond wires that are hanging midair instead of being pinned in place by package epoxy don't vibe with ultrasonic cleaning methods.

The risks are usually small, mind. Which is why prototyping teams and repair shops often use ultrasonic cleaning regardless. But in actual mass manufacturing, you really don't want to risk that extra 1% failure rate. So you either ask the vendors for "safe" values and dance around those energies and frequencies, or avoid ultrasonics altogether.

"...dont vibe with ultrasonic cleaning...."

Quite to the contrary, they DO vibe. Destructively :\

I worked somewhere that accidentally ultrasonically washed a product batch with crystal oscillators in them, and the failure rate was probably even higher than 1%. It was very immediately noticeable when testing the product. There was also an above-average failure rate in the PMIC inductors.

After that, we moved the ultrasonic cleaner to a back room.

Just one XO per board is usually quite safe, but you do get those freaky highly sensitive outliers every once in a while. There are methods to reduce the risks.