For the same reason you can't charge someone with stealing property simply because they possess stolen property. Assumption isn't allowed in evidence.
You can charge them, you just may not be able to convict them. People are arrested and charged with theft for mere possession all of the time.
See Cam Newton.
But isn't this a little different? Personal property can easily be moved around and placed in someone else's possession for purposes of framing them. But a human being that is physically present in a country? What's the excuse there? The Mexican cartel drugged some random hombre and snuck him across the border against his will, all for the purpose of framing him for illegally entering the U.S.?
Is anyone really going to have a reasonable doubt as to whether a person who is not a U.S. citizen, yet is present in the U.S., and for whom there is not a shred of documentation which remotely suggests that he/she was legally present at any point in time, crossed the border by illegally entering this country?
Again, I don't deal with this area of law, so do correct me if I'm wrong, but just from reading a few memorandums from the DoJ, it would appear that individuals who are merely "found" to be residing in the U.S. without proper documentation can be charged with this federal crime; they don't actually have to be caught in the act of illegally entering. There's also some case law which seems to suggest that an individual who is "found" in the U.S. can be charged with illegal entry:
Since 1908, federal courts have recognized that "entering" the United States requires more than mere physical presence within the country. United States v. Pacheco-Medina, 212 F.3d 1162, 1163-64 (9th Cir.2000). To "enter," an alien must cross the United States border free from official restraint. Id. If an alien is not discovered until some time after exercising his free will within the United States, he has entered free from official restraint. United States v. Martin-Plascencia, 532 F.2d 1316, 1317 (9th Cir.1976).
Am I misreading those quotes, or otherwise missing something? (Legitimate question; no sarcasm intended).