The vessel, Orpheon, was Space Pirate in origin, so we can rule out the distress beacon being caused by a Space Pirate attack.
There is information in the logbook that give us insight into the events prior to Samus landing there:
"Escape pod entrance. The vessel has already been jettisoned. Evacuation occurred 6 hours prior to your arrival."
"Zebes has fallen. All ground personnel are presumed dead, either killed by the Hunter clad in metal or in the subsequent destruction of the underground facilities. Our research frigates Orpheon, Siriacus and Vol Paragom were in orbit at zero hour and managed to retreat. Frigate Orpheon is now docked at Vortex Outpost. Orpheon's cargo appears to have a 100% survival rate; Metroids are healthy but on restricted feeding schedules due to uncertain supply status. We are ready to begin research on the Metroids and other promising life-forms. Security status remains at Code Blue; no signs of pursuit from the Hunter." - Fall of Zebes
"Parasite female, genetically enhanced by unknown means. A weak spot has been detected in this creature's mouth. Use your auto-targeting to acquire this new target! Scans indicate the presence of a potent mutagen, origins unknown. Creature exhibits the ability to fire weapon-grade blasts of energy from its mouth, a trait not present in the standard parasite genome. It appears the Pirates have begun a bioengineering program, with considerable results." - Parasite Queen
Let's also look at what some of the poor Space Pirates faced:
"Status >> Death caused by a severing of the spinal cord."
"Status >> Death caused by severe flame damage to the exoskeleton."
"Analysis detects large amounts of blood missing from the carcasses. These bodies may have been used for nourishment. Pattern consistent with predator behavior."
Indeed there were many dead space pirates when we got there, and they all had damage inconsistent with the kind of weaponry in the Metroid Prime universe. We also find a dead Parasite Queen in the Emergency Evacuation Area with 3 escape pods jettisoned. We can infer that the Space Pirates were chased by this Parasite Queen to the evacuation area where some survived, but most of the pirates aboard Orpheon perished. The Parasite Queen roamed freely, and there were plenty of bodies everywhere to feed on. These events occurred just 6 hours prior to Samus's arrival on Orpheon.
Now what about what happened to cause this in the first place? We can only assume the pirates did themselves in. Phazon was present on Orpheon, as well was a number of perfectly healthy Metroids and other creatures. The pirates obviously did plenty of experiments on these creatures, as is evident by the Parasite Queen and plenty of scans aboard Orpheon of the failed experiments. Now there were 2 Parasite Queens that had escaped, the dead one in the evacuation area and the one you fight in the game. While it is possible that other creatures escaped, most creatures were still safely in containment when Samus traversed the vessel and could not do much. We can assume that only the Parasite Queens and the Parasites managed to escape and ravage the frigate.
Based on this, we can conclude that the Space Pirates sent the distress signal around the time they attempted to make their escape.