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Bolton were pressed on the defensive and it was no surprise when Ugo Ehiogu put Boro ahead with a header from a Geremi left-wing corner in the 23rd minute.
After the break Bolton went out to make amends for their disappointing showing, no doubt responding to a rocket from Allardyce.
The Lancashire side were livelier after the break but any chance of pulling the game round was crushed with a disputed Geremi goal.
The Cameroon wing-back broke through and finished with Bolton expecting an offside flag. Their protests to the referee were in vain.
Allardyce summed up: "I am very disappointed at the way the goals were conceded.
"I am told the first was not a corner and the second came at a time when we were pushing forward and having our best spell.
"It is a bit of a worrying time for myself and the team. We are not putting our chances in the net."