Trump tweeted that "Mexico's Soldiers recently pulled guns on our National Guard Soldiers, probably as a diversionary tactic for drug smugglers on the Border", but he didn't support the drug-smuggling claim.
Then came a warning: "Better not happen again!"
His comment comes after the Associated Press reported US soldiers were stopped and questioned by Mexican troops this month, while conducting a surveillance operation on the USA side of the border.
"We are now sending ARMED SOLDIERS to the Border. Mexico is not doing almost enough in apprehending & returning!" he added.
USA troops are already at the border to help reduce illegal crossings.
The command's statement said only that the Mexican soldiers departed the area "after a brief discussion between the soldiers from the two nations". His tweet could signal a shift in the rules of engagement, meaning they have clearance to use lethal force on US soil, which could present legal challenges since they are being deployed for what technically is a domestic law enforcement mission.
"Throughout the incident, the USA soldiers followed all established procedures and protocols", Northern Command said.
He recently said Mexican leaders had provided more assistance stopping Central American migrants from approaching the USA boundary - so much so that it was a major part of his decision to shelve his threat to close legal ports of entry despite warnings of an economic hit.
"We don't want to fight with the United States government, neither do we want to get involved in their partisan political confrontations", said Lopez Obrador.
The Mexican soldiers had reportedly believed that they were on the Mexican side of the border when they were in fact on the American side. "We are not going to allow ourselves to fall into any provocations". Officials said they deported many who didn't have them.
President Trump encouraged Democrats in Congress to take action on border security. "Most of the violence is in northern states and we prefer looking after the Central American migrant population in the south and southeast".
"A very big Caravan of over 20,000 people started up through Mexico".
Earlier this month, Trump threatened to shut down the southern border if the Mexican government did not do more to stop drug trafficking.
The 418,000 number refers to the number of apprehensions reported by U.S. Customs and Border Protection in this fiscal year, which began October 1.
There is, in fact, another caravan traveling through southern Mexico at the moment heading for the US border.
The Trump administration says the policy is one way to reduce the number of asylum seekers being released into the United States for the months or years it can take their deportation cases to be decided.