Jones -- who appeared in New Mexico court virtually -- was charged with assault and interference with communications earlier this week ... after a testing agent claimed he made threats and took their cell phone when they popped up at his Albuquerque home unannounced back in March.

As we previously reported, two drug testing agents for the UFC's anti-doping partners -- Drug Free Sport International -- went to Jones' pad to collect a pee sample ... but in a police report, one of the agents told authorities Jon grew agitated with her after he was unable to provide a urine sample.

The agent -- identified as Crystal Martinez -- told Albuquerque Police she was "terrified" after Jones got into her face and was "afraid Jones would hit her."

The woman claimed Jones was upset with how early they arrived ... and at one point in the interaction, he allegedly said, "Do you know what happens to people who come to my house? They end up dead."

Jones has denied the accusations, saying in a now-deleted Instagram post that while he was frustrated ... nothing threatening was said.

"I want to clarify that there is a video showing both drug testers leaving my home after the testing session, where we exchanged a high five and a hug. Although I was frustrated with the unprofessionalism and used profanity out of frustration it ended friendly and amicably, nothing threatening at all."