My concern, which applies primarily to high-speed long-distance flight, is that the heat exchanger's walls are extremely thin (20 or 30 microns), and the upper atmosphere does contain particulates like organic matter and sand grains blown up from the surface (sand from the Sahara blows all around the world), and on the way to reaching the upper atmosphere a plane flies through dust, bugs, and birds. It will take some flight hours to see if this is a problem, and if so how often, and whether the Sabre engine will be extremely sensitive to foreign object damage.
Since the heat exchanger has almost no mass, it also has almost no inherent thermal mass, so if it fails the compressor inlet temperature will probably rise much faster than the engine can be shut down, leading to very bad things, which might be compounded if the heat exchanger fails structurally and gets sucked into the compressor.
For spaceflight this probably isn't as much of a concern because flights would be infrequent (compared to an airliner), not stay in high-speed airbreathing mode very long, and the runway can be treated almost like a clean room. For passenger flight it's a potential issue. I'm hoping they tested the heatsink against all kinds of abusive impacts (commercial aircraft engines are tested with a chicken cannon, which is entertaining to watch).
If it does turn out to be an issue there are ways to reconfigure the inlet airstream so heavy objects keep going straight past the heat exchanger, which they've already done in part with the ramjet bypass air. It could be that the only problem is that during ground operations, when there really isn't any bypass airflow, a lot of the tubes will get jammed with bug parts, which doesn't sound too bad.