The Lufftwaffe was largely destroyed by D-Day. The Pointblank plan had been conceived and instituted in early 1943. This was a joint Anglo-American campaign to the destroy the Lufftwaffe and German industrial targets. Pointblank was very successful in depleting the Luftwaffe. Eisenhower promised his troops that any aircraft they would see would be allied aircraft. A promise that for the most part was true. Essentially allied forces had depleted the Luftwaffe to near inoperable levels and rule the skies of Fortress Europe.

Source: D-Day the invasion of Normandy June 6, 1944, Randy Holderfield & Michael J. Varhola.

There were German fighters and bombers over the beaches on D day. The official German mission reports for France claim 327 day sorties in the area and 217 night sorties on the night of the 6th - 7th. They claimed to have destroyed 19 allied aircraft and 4 ships vs 20 German planes lost.

E.R. Hooton in Eagle in Flames believes that 127 of these sorties were ground strike or anti-shipping missions at Normandy.

For comparison the Allies flew over 14,000 sorties during the same period. So while there was some German presence, it was completely overshadowed by the Allied air forces.

Edit: I miss read the question. But I'll leave that part up as it is peripherally applicable.

To answer the real question. No, the Germans didn't try to bomb marshaling units. The Germans did launch an air campaign from Jan-May 1944, Operation Steinbock. But they were raids against cities staged in retaliation of Allied bombing of German cities. In fact many of the individual raids were named after bombed German cities to commemorate them. The raids focused mostly around London.

The Germans were also still launching anti-shipping bombing raids out into the Atlantic in early 1944. So between that and Steinbock, there weren't any units left to focus on troop gatherings.