Assumptions
- Chemical explosives probably aren't going to deliver the energy density to achieve ghosting on walls. Perhaps a very large fuel-air explosion may satisfy the energy requirements but this would need to be a controlled detonation, not an accident. And if controlled, why follow up with a nuke? Also, chemical explosives don't completely vaporize the bomb casing when they go off.
- Neutronic fusion and fission reactions leave behind significant radioactivity so those won't work. Also, these explosions don't leave behind fragments.
- Aneutroic fusion provide plenty of energy without neutrons. That's promising for radiation. They won't leave fragments either.
- Antimatter reactions certainly have enough energy delivery. This Physics SE answer seems to say there won't be any long term radiation. Antimatter reactions are definitely energetic enough to vaporize the casing so no fragments.
- Bias of the investigator is that this was a deliberate alien attack.
Possibilities for Fragment Origination
Since the fragments are a uniform size they should come from a part of the bomb/vessel that has a uniform thickness and strength, probably the casing/hull itself.
So what happened to the other parts of the vessel/bomb? If a vessel then what happened to the engines? In practically all terrestrial engines, they are the strongest parts of any vessel because they have to withstand the most concentrated energies. In every picture of an airline crash I've ever seen, the engines are either recognizable or virtually intact. They don't break easily. So either this delivery mechanism had no engines (entirely possible in the case of a bomb) or the engines were vaporized on detonation...possible but this precludes chemical explosives.

Fragmentation weapons don't make sense in a weapon employing this magnitude of energies. The thermal, overpressure and possible radiation effects far outweigh any fragmentation damage.
Perhaps there were two explosions? A smaller chemical explosion that blew off the casing then an aneutroic fusion or antimatter reaction that vaporized the engines.
Reasoning
If manned then engines must be present because a crew will want to escape/move thus requiring engines.
If bomb and manned then weird aliens and we are in big trouble because death doesn't mean anything to them. Kamikaze!
If smokeless reentry then intentional positioning or special hull. An uncontrolled descent through the atmosphere will most likely result in smoke.
If special hull that can handle reentry then unlikely to shatter under mere chemical explosions. If the hull did shatter under a chemical explosion then this will require more explanation and fine tuning.
If chemical then fragments is easy but no ghosting.
If antimatter then ghosting is easy but no fragments.
If aneutroic fusion then ghosting is easy but no fragments.
Sequence:
Station keeping over Philly.
Malfunction causes chemical explosion creating and spreading fragments. Happens at tens of thousands of feet. Station keeping ability lost and fall commences.
Vessel falls to approximately 1500 feet then detonates the engine/reactor in fusion or antimatter explosion causing the hull to vaporize and ghosting of humans on the surface. Killing lots of aborigines is preferable to letting advanced technology fall into their hands. All crew are vaporized too. Or, the earlier chemical explosion caused a failure cascade the lead to a failure in their fusion or antimatter plants leading to the second larger explosion.
Detonation causes devastation described by the OP.
Constraints to satisfy
Several human shadows printed on walls and ground at the crash site.
The bomb breaks apart with pieces as big a mobile phone littered everywhere. The spread of these fragments is unknown. No other fragments were recovered.
Radiation level normal.
Manned munition.
Bomb delivered from orbit without any kind of smoke or re-entry trail.
Detonation leveled a metropolitan area of 1.5 million people.
Blast strength approximately 30kt to achieve the 1km leveling of buildings.
Constraints satisfied
- Yes. See 3.
- Yes. See 2.
- Yes. See Physics SE answer.
- Yes. See 1.
- After controlled descent and station keeping, there is no smoke trail. A special hull may prevent a reentry smoke. Also, the ship may utilize an engine beyond our understanding that allows controlled deceleration from orbital speeds to terrestrial speeds.
- Yes. See 4.
- Yes. See 4.
What about the first explosion?
If the explosion was small enough and high enough, it's possible that no one outside the blast radius of the later, larger explosion survived to tell about it.
If a bomb...
Then it's unusual to have a two stage weapon with a long enough delay between first burst and main burst for casing fragments to clear the vaporization zone. Fuel air weapons and cluster bombs have this kind of delay but they are also not powerful enough to vaporize the casing but they do have two stage attacks. Spreading fragments when equipping a nuke doesn't make sense unless the fragments were intentionally seeded in which case further investigation into the fragments is required.
Also, if a bomb, why Philly? There are plenty of more important places to destroy first. Any alien who's even halfway paying attention will know that Philly isn't a major transit hub or seat of political power. If this is an intentional attack then we should look for more attacks.
Conclusion
This was an accident, not a deliberate attack. Baring any additional evidence from the site or contact from the aliens, evidence points to this incident as an accident.