Assuming the timetable is mistaken one other possible explanation I can think of is that the timings are supposed to be emboldened and with a * to denote the train is being looped rather than the error being a timing error. I do not know if the timetable is in error, though.
I've got a copy of the same timetable (Section YJ, May 1989). I believe it's minor error based on the following:
Where other trains are given pathing time between Rotherham Masborough and Aldwarke Junction (for example on pages YJ7 / YJ8), this is shown in the blank space between the two locations. The line used is indicated (ML for main line or BHL for Barrow Hill line) followed by the pathing time in minutes inside a circle.
For example, 6E68 08:53 WSO from Peak Forest (on page YJ8) passes Rotherham Masborough at 10:05 and Aldwarke Jn at 10:20. The additional time is explained by the ML (10) note in between - runs main line with 10 minutes pathing allowance. Also of interest for that particular train, the time at Aldwarke Junction is 10x20, indicating it crosses from the Down Main to the Down Pontefract at Aldwarke Junction. Meanwhile, 7E03 12:00 FSX Betteshanger to Scunthorpe CHP passes Rotherham Masborough at 10:15 (Barrow Hill line) and Aldwarke Junction at 10:18. These movements potentially conflict at Aldwarke Junction (on Wednesdays at least!) and the pathing allowance on 6E68 means it passes Aldwarke Junction after 7E03 instead of before it.
If the 7E89 you were looking at had a similar pathing allowance, it should be indicated with a circle, and show 03:16 passing Aldwarke Junction on both tables. The need for 12 minutes pathing time at 3am on a Monday morning seems doubtful, so I suspect this was unintentional.
In the Chesterfield - York table adjacent to 7E89 is a 6E57 passing Aldwarke Junction at 03:16 TThSO. It's possible that someone read across from one train to the other when timing 7E89 through Aldwarke Junction, leading to a twelve minute discrepancy, but that's just a guess - I'm not sure what timing methods were being used at the time. As the only consequence would have been 7E89 getting to Down Decoy slightly earlier than planned, the driver would have been happy and I doubt anyone else paid much attention to it!
On the subject of timing discrepancies, I saw a weird one in TRUST a few years back. I can't remember the exact details, but the train effectively went "back in time" on the schedule (not a clock change issue but a similar effect). When the timings were uploaded to TRUST, they were sorted into time order, meaning that the schedule jumped forwards and backwards between locations in an impossible sequence. With changes to software I don't know if that's even possible any more...
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As for Aldwarke Junction itself, 1989 is significant as this was the last year before the remodelling of Aldwarke Junction in 1990. Aldwarke Junction itself came into being in 1965, in connection with the opening of Tinsley Yard. Before that, the former Great Central route from Mexborough to Rotherham Central was completely separate from the Midland lines running nearby. Also of note is that the current "Swinton Curve" was closed between 1965 and 1990.
Aldwarke Junction is disussed in Chapter Five of
Tinsley and the Modernisation of Sheffield's Railways by Chris Booth and Alex Fisher:
[1965 changes]: New tracks connected the GCR lines to the "slow" lines of the MR in the direction of Leeds and conversely the "slow" lines of the MR to the GCR, in the direction of Mexborough.
[1990 changes]: The MR lines between Masborough Station North Junction and Aldwarke Junction were reduced to double track, with the removal of the former main lines. The GCR lines between Aldwarke North Junction and Aldwarke South Junction were also removed...
This is a great photo of Aldwarke Junction (and signal box) taken in 1986, looking south:
https://www.flickr.com/photos/auchlander/6806463246/ (Photo: Auchlander)
Another 1986 view of the junction with the steelworks at Aldwarke (part of BSC Rotherham) in the background:
https://www.flickr.com/photos/auchlander/6806463706/ (Photo: Auchlander)
Video of freight trains passing Aldwarke Junction in 1987 (camera is looking at the GC lines - see video description for details of the trains to help figure out which direction is which):
Trackside Treasures | Archives 1987. Aldwarke Junction. Compilation 46. Mixed footage
