Why is the AI randomly scrapping facilities on my planets? I have sufficient funds.

You need to have sufficient funds before the facilities are scrapped. The AI will scrap until you are solvent. Building new facilities or ships that put you over your command rating can cause your cash flow to go negative. I don't believe the AI will scrap ships for you but will scrap facilities. Losing a planet or getting hit by a random event can also change your BC situation in between turns. So can dismissing a leader or having a change in the status of one or more trade treaties.

The other instance where the game will scrap facilities is one where the BC's you have are irrelevant. If you have previously built a processor or renewer and then build a waste dump the pre existing facilities get scrapped as they are redundant.