USB-C superspeed Signal pass through connection issue
5 Gbps (or 10?) is no joke. Very small impedance discontinuities can badly impact the signal integrity.

The biggest problem I see here is lack of return path vias where signals transition between top and bottom layers.

Whenever the signal transitions from layer 1 to layer 4, the return currents beneath the microstrips need to transition from layer 2 to layer 3. This means one or more ground vias are needed near every signal via. A transition without these vias will present an inductive discontinuity, and also likely cause radiation as return currents find a path between the ground planes.

In addition,


USB high speed and superspeed are specified with 90-ohm characteristic impedance, not 100 ohms. In the last few millimeters before a termination, a 11% error in Z0 might not be a big issue, but for a board placed in the middle of the overall signal path it could be a real problem. You should design the trace geometry to target 90 ohms.
You haven't told us whether you specified the board fab should be responsible for controlled impedance or if you just specified the geometry and stack-up. If you haven't given the fab responsibility for impedance, then variations in copper plating thickness, prepreg thickness, etc., could be causing variations in Z0 that are out of your control at layout time.
You haven't told us your material spec. Just asking for "FR-4" could result in substantial variation in dielectric constant, invalidating your calculated characteristic impedance. You should use a material with a well-defined Dk, and specify it by the laminate vendor's product designation (for example, "Isola FR408 HR"). If you're specifying geometry rather than Z0, you should specify the material glass weave and resin content (after making sure your desired material is available to your fab shop). 
Your traces are close enough together that there could be cross-talk between them (this also depends on the dielectric thicknesses that you haven't shared). Return currents sharing transition vias could also contribute to cross-talk.