You're right to be concerned; this is a seriously problematic and potentially dangerous installation. While you're having trouble finding one specific code section that explicitly prohibits this exact scenario, that doesn't mean it's acceptable. Here's a breakdown of the issues and relevant code principles, even if a "smoking gun" code section is elusive

Why This Is Wrong (Beyond Just "Feels Wrong"):
Unequal Impedance/Voltage Drop

This is the biggest problem. Aluminum has a higher resistance than copper. Even though the aluminum conductors were sized to carry the same current, the voltage drop along the aluminum conductors (A & C) will be significantly higher than the voltage drop along the copper conductors (B & Neutral). This means the voltage supplied to loads connected to phases A & C will be lower than the voltage supplied to phase B. This voltage imbalance can damage sensitive equipment, especially motors. Motors rely on balanced voltages to operate efficiently and safely. An imbalance leads to overheating and shortened lifespan. Consider a simple motor operating from phases A & B. Since phase A voltage is lower, the effective load across the motor is effectively unbalanced, and the motor will overdraw current until failure.

Harmonic Distortion Amplification

Unequal impedance can also exacerbate harmonic distortion problems on the system. Harmonics are generated by non-linear loads (electronic devices, LED lighting, etc.) and can cause overheating of the neutral conductor and other equipment. Unbalanced impedance allows these harmonics to circulate in unpredictable and damaging ways.

Overheating

While you sized the aluminum for the ampacity, different thermal conductivity characteristics between aluminum and copper will result in different heat dissipation rates. You could have localized overheating in connections and terminations even if the overall current doesn't exceed the conductor rating.

Safety Hazard

Uneven voltage distribution leads to unpredictable system behavior, increasing the risk of electrical shock and fire. A fault on one phase could have very different consequences than a fault on another phase.

Future Maintenance Nightmare

This setup will be confusing for anyone working on the system in the future. Troubleshooting will be much more difficult.

Relevant NEC Principles (Even Without a Direct Prohibition)

While the NEC doesn't have a section that explicitly says, "You cannot use aluminum for some phases and copper for others," the following general requirements are violated:

NEC 110.3(B) - Installation and Use

"Listed or labeled equipment shall be installed and used in accordance with any instructions included in the listing or labeling." Most equipment (breakers, panels, etc.) are listed for use with copper conductors or aluminum conductors, not a mix.

NEC 110.5 - Conductors

Although there is no explicit prohibition, all equipment must be listed and labeled to suit the installation as outlined above.

NEC 215.2(A)(1) - Feeders

Requires feeders to have sufficient ampacity for the calculated load. While you've addressed the ampacity rating with the larger aluminum conductors, that doesn't solve the voltage drop/impedance problem.

NEC 215.2(A)(3) - Voltage Drop

While not mandatory, it provides guidance on voltage drop. The commentary following the section makes the principle of balanced voltage drops clear.

NEC 220 - Branch-Circuit, Feeder, and Service Calculations

While focusing on load calculation, this article reinforces the need for balanced loading across phases, which is undermined by mismatched conductors.

NEC 300.3(B) - Conductors of the Same Circuit

"All conductors of the same circuit...shall be contained within the same raceway, cable, or otherwise run together." This is often interpreted to ensure that all conductors experience similar environmental conditions, which is important for impedance balance. The intent is for similar behavior. While technically the conductors are likely run together, using different materials defeats the purpose of this section.

NEC 310.15(B)(3)(a) - Neutral Conductor

While not directly applicable, this section addresses situations where non-linear loads are present. The higher impedance of the aluminum conductors would exacerbate the problems associated with harmonic currents on the neutral.

NEC 408 - Switchboards and Panelboards

Requires proper labeling and grouping of circuits, which becomes problematic with this non-standard configuration.

NEC 430 - Motors, Motor Circuits, and Controllers

As mentioned earlier, voltage imbalance is detrimental to motors. This article highlights the importance of providing balanced voltage to motors.

The Inspector's Argument

An inspector could reasonably argue that the installation violates 110.3(B) because the equipment is not being used according to its listing (which is likely for either all-copper or all-aluminum). They could also cite the general principles of good electrical practice and the potential for unsafe operation.

What to Do

The only correct solution is to replace the conductors with either all-copper or all-aluminum of appropriate size for the entire run. Do not attempt to "fix" this by adding impedance-matching devices or other band-aids. Document the problem thoroughly and immediately notify the contractor that the installation is unacceptable and must be corrected. If they are resistant, contact the electrical inspector and involve them immediately.

In Summary

While you might not find a single, crystal-clear code section saying "no mixing Cu and Al phases," the principles of electrical safety, voltage balance, impedance matching, and proper equipment installation are all violated. This is a dangerous situation and must be corrected.

Disclaimer: This information is for educational purposes only and does not constitute professional engineering or legal advice. Consult with a qualified electrical engineer and the local authority having jurisdiction (AHJ) for specific code interpretations and requirements in your area.* Flag for review