Date: 201604
Local time of day: 0601-1200
Location: MKE.TRACON, WI
Flight conditions: VMC
Light: Daylight
Aircraft: Airliner 99
Operator: Air Taxi
Operating under: Part 91
Flight plan: IFR
Mission: Cargo / Freight / Delivery
Flight phase: Climb
Airspace: Class C MKE
ATC / advisory: Tower MKE
Second aircraft: PA-31T Cheyenne I
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Second reporter function: Approach
Anomaly: Deviation - Altitude Excursion From Assigned Altitude; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Detector: Person Air Traffic Control
Result: Air Traffic Control Separated Traffic; Air Traffic Control Issued New Clearance; Air Traffic Control Issued Advisory / Alert
Contributing factors: Airspace Structure; Human Factors; Procedure; Manuals
Primary problem: Human Factors

Narrative: I was training a developmental on Local Control during the morning cargo outbound; when we accepted a point out on an aircraft descending to 4000 feet. My developmental had two departures; one rolling; one holding short. The aircraft on the ground was issued 'Climb via the SID; except maintain 3000 feet.' Once aircraft was airborne; developmental said to Aircraft X; 'Climb via the SID; except maintain 3000.' Aircraft X (garbled or stepped on response) was questioning whether to climb via the SID and not to 050. I said to my developmental; 'oh; I bet he was cleared via radar vectors; not the SID.'We have the option on Clearance Delivery to issue the prop aircraft vectors to first fix or SID. So; I had the developmental say; 'Climb and maintain 3000; turn right heading 330.' The other aircraft then was issued a similar clearance; since Clearance Delivery said they had read the clearances with Radar Vectors not the SID that morning. The departure controller then experienced the confused pilot deviating from the 3000 foot assigned altitude and climbing into Aircraft Y level at 4000 feet. Management was advised about the issue of not knowing on Local Control how Flight Data/Ground Control issued the clearance and not knowing what phraseology to use to amend an altitude.The SID is a worthless SID for all aircraft; but especially a prop aircraft; exempt from Noise Abatement procedures. I recommend immediately requesting all controllers issue one or the other. Either all of us shall issue the SID; or preferably; all of us shall use Radar Vectors when clearing these props (numerous cargo props this time of day). Long term; I think either the SID needs to be removed from our SIDs or the required phraseology to amend an altitude from Local Control should leave out the 'Climb via SID; except maintain (altitude)' portion and simply be; 'Maintain (altitude).' Thank you for your time and attention to this; as this procedure most definitely contributed to a pilot deviation this morning; following by two aircraft in unsafe proximity to one another!


Second narrative: Aircraft X was given to me from east feeder level at 6000 feet. I coordinated with tower to descend to 4000 feet. I turned Aircraft Y 10 degrees right to turn slightly away from tower airspace and descended them to 4000 feet. Aircraft X departed on a 330 heading climbing to 3000 feet. I radar identified Aircraft X; turned them to a 360 heading and reiterated maintain 3000 feet.The collision alert went off as Aircraft X was almost to 3000 feet and Aircraft Y was at 4300 feet. I assumed Aircraft X was leveling at 3000 feet and diverted my attention to other duties. As the controller on asked me if I was alright with these two aircraft I noticed Aircraft X climbing through 3600 feet and Aircraft Y at 4100 feet. I immediately issued traffic and the descent to Aircraft X; he saw the traffic; I advised him to maintain visual and descend to 3000 feet. I also pointed the traffic out to Aircraft Y who never saw Aircraft X. Later in the session I gave Aircraft X the brasher warning and he openly admitted to making the mistake. Apparently there was some sort of confusion from the tower's altitude instructions.


Synopsis: A departing BE99 aircraft assigned 3;000 feet climbed to 3600 feet conflicting with 4;000 foot crossing traffic.