|Khizr Khan and wife Ghazala.|
First, per Raw Story, an unnamed spokesperson from Customs and Border Protection says that the US doesn't contact citizens, or noncitizen residents, before they leave the country to warn about travel privileges being "under review."
Sounds right to me. Even at the heart of the early post-9/11 days under BushCo, I never heard of such a thing. (We're ultimately at he-said, she-said on that.)
Second, per The Week, Trump's latest travel ban executive order does not affect either residents of Pakistan or American citizens. Khan is a naturalized citizen and a native of Pakistan. Yes, Muhammad Ali Jr. faced his own problems with Customs two weeks ago, though CPB says there was no religious angle.
It's really hard in general, in fact, to figure out how much of the new barrage of complaints against Customs is real, and grounded, how much is semi-real, but still within its traditional scope of operations, and how much is groundless. Per the Wiki page about the two Khans, if he wanted to exploit the current environment, he could.
So, who knows?
Third option is that some Customs employee said this, but it was purely personal, or even "having fun." Stay tuned.