[4] Habitat restoration has also attracted birds to the center that cannot be seen anywhere else in the continental US, such as green jays and chachalacas,[6] and the grounds are home to bobcats, armadillos, coyotes and tortoises.

"[2] In late July 2017,[10] a National Butterfly Center employee was surprised to discover a bulldozer crew clearing vegetation with a chainsaw and a brush mower, in an area that had been restored with native species from its earlier use as an onion field.

[11][6] On August 1, 2017, the chief of the Border Patrol's Rio Grande Valley sector indicated that although Starr County, Texas, was his first priority for a wall, the nearby Santa Ana National Wildlife Refuge had been selected instead for initial construction, because its land was owned by the government.

[7] In a December 17, 2018, opinion piece in the Washington Post, the center's nature photographer and outreach coordinator expressed concerns about the loss of habitat and disruption to nocturnal species, and said: Right now, in Mission, Texas, we don’t worry about immigrants who crossed the border illegally or drug smugglers.

[13][14] Soon afterwards, however, President Trump declared a National Emergency Concerning the Southern Border of the United States, which the administration claimed invalidated the restrictions imposed by Congress.

"[16] After a QAnon conspiracy theory spread on social media that the National Butterfly Center was smuggling migrants into the US, in late January 2022, Republican Congressional candidate Kimberly Lowe and her purported Secret Service Agent[17] visited the center referring to "the rafts with the illegal crossing" and to child rape, then reportedly injured the director, Marianna Trevino Wright, and almost struck her son with their vehicle.