Date: 201908
Local time of day: 0601-1200
Location: ZZZ.ARTCC, US
Aircraft: Citation Excel (C560XL)
Operator: Air Taxi
Operating under: Part 135
Flight plan: IFR
Mission: Other Repostion
Flight phase: Climb
Airspace: Class E ZZZ
ATC / advisory: Center ZZZ
Reporter organization: Air Taxi
Reporter function: Pilot Flying; Captain
Reporter qualification: Flight Crew Rotorcraft; Flight Crew Multiengine; Flight Crew Instrument; Flight Crew Flight Instructor; Flight Crew Air Transport Pilot (ATP)
Human factors: Communication Breakdown
Anomaly: ATC Issue All Types; Deviation - Altitude Excursion From Assigned Altitude; Deviation - Altitude Overshoot; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance
Detector: Person Flight Crew
When detected: In-flight
Result: Flight Crew Returned To Clearance
Contributing factors: Procedure; Human Factors
Primary problem: Procedure

Narrative: The flight was from ZZZ to ZZZ1. Our company scheduled departure was for XB:00Z. The departure time on the filed flight plan was XA:30Z. Our engine start was at approximately XA:05Z. My FO (First Officer) copied our IFR clearance. I watched and listened as he wrote it for verification. I have photo of the initial clearance as it was copied. After the FO had read back the first clearance; the clearance controller indicated that the read back was correct. The initial clearance given has a great bearing upon; and is a root cause element of our deviation.Our actual takeoff time was XB:13Z; more than an hour after engine start; which also affected cause for our deviation; the clearance was re-issued; but without a full read. We were told we would be about number 35 for takeoff as we began our taxi. During our taxi; we were lead to various parking positions as other traffic taxied around us. We were directed to switch to clearance twice for rerouting while waiting in the various parking positions; and to return to Ground frequency; with no need to monitor the Ground frequency while accepting new clearances. When receiving the last (third) clearance; the Controller told us that it was the same as our first clearance issued. He **did not read** the full original clearance; and did not ask for it to be read back in full. He did say the clearance was the same as the original clearance and contained the Woodstown (OOD) VOR fix. If the original route clearance; ZZZ-OOD-HAYDO-TEBEE-SBY-ZZZ1; is copied and mapped; it would require about a 180 degree turn at HAYDO; and another turn of close to 180 degrees at TEBEE. I believe with some certainty that the clearance should have been ZZZ-OOD-TEBEE-HAYDO-SBY-ZZZ1.Up until a few seconds shy of the time of the deviation; our aircraft was under autopilot and flight director control. We had just been cleared for a short climb; 16;000 ft to 17;000 ft. After the climb clearance; 17;000 ft was selected in the altitude selector. As we neared to 17;000 ft; my PFD (Primary Flight Display) HIS (Heading Situation Indicator) indicated to me that a turn of about 180 degrees was about to commence. Alarmed at this; I disengaged the autopilot; without time to respond to the level off at 17;000 ft. I quickly figured out from our MFD (Multi-Function Display) map that our clearance route points had been reversed. Soon after we received an RA (Resolution Advisory) due to the excessive climb. Almost simultaneously; our Center Controller again instructed us to level off at 17;000 ft. We were just shy of 17;800 ft before returning to 17;000 ft. The autopilot/FMS/FD was commanding a turn of near to 180 degrees at HAYDO to return to TEBEE.Had the routing TEBEE-HAYDO sequence not been reversed; there would have been no issue; and the flight would have continued without consequence. Possibly; had the clearance Controller read the full third clearance and/or had us do another read back; the issue could have also been mitigated so no altitude deviation occurred.




Synopsis: Air taxi Captain reported ATC issuance of incorrect routing and an altitude deviation.