Why is Tell locked back into a military prison?

I had the exact same question after watching the movie. "Oh, I'll look up on the Internet what explains this" I thought, as I was sure someone else must have had the same question. Turned out, even the most brilliant reviews of the movie just glossed over this peculiarity, "Tell goes back to military prison, and then..." It was very frustrating. Never found anybody even mentioning this until I came across your question. So, first, thanks for asking this.

Now, onto an answer. Here's how I would explain it. First, there's absolutely no, as in zero, legal basis for sending a civilian who committed a crime against another civilian (though even that is irrelevant) to the USDB (United States Disciplinary Barracks). The flimsiest and most remote way this could even come close to his being sent back to the USDB at Leavenworth, would be if Tell were charged and convicted under federal law (though it's not even clear why this would happen as his murder of Gordo doesn't meet any of the requirements for such a charge), but even if he were, he wouldn't be sent to the USDB: he would just be sent to the federal penitentiary at Leavenworth. So, I would argue any answer to your question has to dispense with the possibility that there is any way this could actually have happened. This is very important for my actual answer.

So, here's the actual answer. I want to preface this answer first, though, by making sure you are familiar with Schrader's entire oeuvre. It's important that you not take this as some kind of schlocky plot device. My explanation is consistent with the themes of this movie (forgiveness, redemption, and most importantly the impossibility of achieving those AND enjoying happiness--you have to make a choice sometimes, perhaps always, between the two ends). Also, in terms of the plot, so many if not all of Schrader's movies have similar endings to The Card Counter (or at least my explanation of it, which, I promise, is coming up, though you may already have guessed it): from The Taxi Driver to The Last Temptation of Christ to First Reformed: did Bickle really become a "hometown hero" for murdering a pimp and then beating the charges? (unlikely) Jesus, apparently, really did die on the cross, but there is ambiguity about what is real and imagined until the very end. First Reformed ends similarly with distortions of physical possibility (the levitation).

So, now we get to The Card Counter. One reading that explains the ending is that Tell didn't survive. Note that he calls "emergency services" to do what...ask for an ambulance? No, to report a homicide. In other words, there's no urgency to send medics...the subject is already dead...and it's Tell. His last vision is the vision of the impossible conjunction of redemption and reconciliation. Most reviewers focus on the fingers on the glass when LaLinda visits. But, this focus misses the point. Tell doesn't actually want the contact (rooted ultimately in eros and not agape) with LaLinda--hence the glass. If someone has a fantasy (and again I'm positing that this is his "last minutes of life" vision of bliss), they don't need to put up a glass to separate them from the object of their desire. The glass that separates Tell from others is part of his fantasy. His reconciliation and the happiness it provides him (impossible in reality) come from his return "home"--his impossible return to the same prison where he was once fully himself. There's more that could be said here along lines of other Christian themes--physical suffering, taking the place of another in punishment, etc.--that also come up in other of Schrader's movies. But I wanted to make clear primarily how the return to the same military prison really has no other explanation but the one that I've given.