Beams. The German navigation beams were detected in good time, but it was only the 1st or 2nd time the "Aspirin" jammers were used in anger. One was almost exactly under the beam but its frequency was slightly inaccurate and the jamming was ineffective.
Ultra. There was
AFAIK an Ultra decrypt referring to a major op coming up called "Moonlight Sonata" but it didn't mention the target, so not really much use. Anyway, there would have been no need to "protect Ultra" over the issue of the X-Gerät beams as they could, of course, be detected by radio monitoring. Note, I'm not sure in my mind whether Knickebein or X was the system involved, but non-Ultra intelligence tipped us off about both. Knickebein was betrayed by a combination of ESM and POW interrogation - as well as the incident in Hyde Park where a German Nav bailed out and found on landing that he still had a notebook with various nav information on him, including freqs for something called "Willi Knickebein" with two stations and the times it would be radiating. He tore it up into some 3,000 pieces and was trying to bury them when Plod intervened. RV Jones spent a night putting the bits back together...
X was discovered by the examination of a downed He 111 fitted with the receiver. Unlike Knickebein, which used the Lorenz blind landing technology on a bigger scale, X-Gerät needed more complicated electronics and visual presentation.