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Metrolinx says a series of events lined up to make for "horrendous delays" for many travellers on Wednesday.
Passengers on GO's Lakeshore East, Lakeshore West and Stouffville lines were held up, some stranded as long as two hours.
Spokesperson Ann Marie Aikins says it started in the afternoon when bits of concrete fell onto the train tracks from the Kennedy Bridge above where a city crew was doing work.
The Lakeshore East Line was closed as crews checked that the bridge was structurally sound. The line was gradually re-opened, but debris still kept coming down. Again, traffic was stopped, the bridge inspected, deemed safe and trains started to roll again, albeit slowly.
But then Aikins says there was another "operational issue" with one of GO's lines that caused more delays.
GO's backups were compounded by an unexplained operational issue at Via Rail on Wednesday night. Because GO and Via share tracks, some of GO's trains were left stranded. Aikins explains some trains were able to back up into Union to let passengers off to find another way home.
"We've got our TTC protocol in place so they can use their passes and their PRESTO cards to get on a TTC, but this has just been a very unfortunate evening for many of our customers", says Aikins.
VIA Rail, who also reported issues, said for 'some reason' a Kingston-bound train that was originally scheduled to leave at 5:30 and then pulled out of the station at 6:15pm, was told to stop and back up all the way to Cherry Street, before finally pulling out for good after 8 p.m.
Spokesperson Mylene Belanger says they are investigating why that delay took place.
All the issues are expected to be resolved by Thursday morning's commute.