Services through Argyle Street were disrupted after a train broke down at about 7.50am and technical problems triggered problems between Cardonald and Glasgow Central.
Scotrail's website warned of "severe disruption" for passengers at Argyle Street.
The company said the train was back on the move by 8.25am, but there were some knock-on delays as a result of trains being out of position.
Rail passengers travelling from Ayrshire faced delays between Cardonald and Glasgow Central due to two separate issues on the line.
An unavailable member of train crew combined with a triggered warning signal resulted in the problems.
Scotrail said a member of train crew was unavailable and a train within Shields depot, not in passenger service, triggered a warning signal in error.
The second issue resulted in some trains within the local area being brought to a halt as a precaution.
Scotrail said it was established within a few minutes that this was a false alarm, and trains were able to proceed.
But, there was some knock-on delays as a result.
One passenger, travelling from Johnstone, said he was delayed more than half an hour by what train announcements described as a "technical fault."
A spokesman said: "An error in the depot contributed to disruption this morning.
"We're investigating what happened and sincerely apologise to customers who were delayed as a result."
Meanwhile, a crash on the A725 East Kilbride Expressway at Blantyre caused delays for eastbound motorists.
Two cars were involved in the incident, between the A724 junction and the Raith Interchange, which happened at around 8.10am.
Police and the ambulance service were at the scene but there were no reports of any serious injuries.
The delays follow problems on the roads and railways earlier in the week.
Heavy rain on Monday night caused flooding across west Scotland resulting in chaos of commuters on Tuesday morning.