Some wildlife populations move around as the habitat changes seasonally, and obstructing their movement could cause them to starve.
In addition, dividing populations sets them on the path to speciation. True, speciation takes tens of thousands of years...
Do you recall reading the threads about what prevented storm surge barriers from being built to protect New Orleans in the 1970s? Yep - wildlife activists filed a federal lawsuit against the US Army Corps of Engineers and tied up the funding until the USACE relented and spent the money on other projects.
I hope we learned something from that, but I still give this wall project about a 50% chance of being completed. Trump better have all his counter-measure moves planned.