The Sun's article starts with this passage:
The youngster, 12, died at the scene of the accident in Glenaylmer Road, Kelloholm, near Sanquhar, around 4pm yesterday afternoon.
But officers confirmed that he was severely injured by the telephone style pole and later died at the scene of the accident.
Today a bunch of flowers were left at the scene, with the message inside reading: "Fly high Keiran. Miss you so much."
The writer seems to be talking about a single bunch of followers instead of bunches of flowers, because a single message inside the bunch is mentioned.
So, I wonder why it's "were" not "was".
Now, let's change the context a bit, forget about the message, and assume that different people left two or more bunches of flowers at the scene. In this context, I think you can say "Today many bunches of flowers were left at the scene" or even "Today a number of bunches of flowers were left at the scene".
In this case, can you still use "a bunch of flowers" to refer to "a number of flowers" and treat the noun phrase as plural as follows?
Today a bunch of flowers were left at the scene.
No. A bunch of flowers was left at the scene. The "of flowers" just tells you what the bunch was composed of.
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No. A bunch of flowers was left at the scene.
The "of flowers" just tells you what the bunch was composed of.
You could easily substitute more inclusive word, such as "a posy" or "a bouquet" for "a bunch of flowers" and those would obviously be singular. A bouquet was left at the scene.