All fluids have what is known as a minimum vapor pressure at a given temperature. At pressures below this level the fluid itself begins to boil, or "outgas". I suspect this is the issue with your vacuum process with the hydraulic fluid; and, you are at some point, in addition to air, you are evacuating the vapor state of the hydraulic fluid itself through your vacuum pump. If this is the case, after a while, you should start to see some traces of condensed hydraulic fluid at your vacuum pump discharge.
Your hydraulic fluid manufacturer should be able to provide you with your fluid's vapor pressure data.
As to the issue with bare metal, that one is beyond my knowledge.