Angela, Hodgins and an FBI team inspect the site that a tornado went through 5 weeks prior where they suspect the murder happened. The area appears as if the tornado just touched down a couple days before. There had been no cleanup efforts in 5 weeks.
When Hodgins is explaining the tensile strength of the broken glass sample to Saroyan, he gives a value of 2.63 grams per cubic centimeter, which is a value for its density, not tensile strength, which is measured in kilograms (force) per square centimeter (area).
The rainbow after the tornado is in the wrong place in the sky for the direction of the sun. Rainbows ring around the anti-solar point, that is, the point directly opposite the sun, and usually have a 42 degree radius making their rainbow too high as well.
The tornado remains over the storm cellar much longer than it really would. A tornado would normally pass over in less than 5 minutes unless it "stalled" yet the sequence lasts about 7 minutes. If it had stalled there would have been far more damage to the vehicles than there was.
When you see Michael in the crib asleep, when he stirs and rolls you can clearly see a label on his pacifier that has the name Noah which is the name of one of the twins who play him.
Booth and Sweets are going to track down some storm chasers in North Carolina and are almost there. Booth is talking to Bones on the phone and she is in Booth's apartment in DC. Booth arrives at the storm chasers site, starts to question them and goes into the shelter, (about 10 minutes pass). Then Bones shows up at the shelter immediately after everyone gets inside. North Carolina is at least a 4 hour drive from DC and Bones got there in maybe 20 minutes. Bones then leaves Booth and Sweets 4 hours from DC to find their own way home.
As a true Rock God, Angela's father should be well aware babies suffer hearing loss just as adults do. As she has no apparent effects, even after "being on tour" as an infant, it follows Michael should be shown wearing protective ear gear.