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The Trotters thought that they should have been awarded two penalties midway through the opening period when Zach Clough and Craig Conway both went down under pressure in the box, but the referee was not interested in their appeals.
Jordan Rhodes started to pose a threat in the Bolton box for Blackburn on his return from injury, but the Scottish international twice headed over following promising crosses from Conway and Ben Marshall.
Blackburn were on the hunt early in the second half, with Marshall unleashing a low strike which was blocked by Prince Gouano, before Conway saw his follow-up deflected over.
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The visitors were soon pressing down the other end though, with Wellington running at the Blackburn area before curling an effort towards the top corner, but he lacked the accuracy to test David Raya.
Amos had to make the first save of the night almost 70 minutes into the tie as Spurr whipped in a dangerous-looking free kick, but the Bolton keeper was able to tip it over, before Mark Davies made a clearance off the line to deny Spurr from the resulting corner.
Both sides started to show an increasing urgency as the game headed into the final 10 minutes, with neither side having secured a win in the league this season coming into tonight's tie.
Blackburn briefly thought that they had opened the scoring when Bengali-Fode Koita put the ball in the back of the net after a Rhodes effort was blocked, but the substitute's low strike was chalked off for an offside in the build up.
Bolton immediately charged down the other end where Emile Heskey almost powered it home for Neil Lennon's side, with Raya palming a cross into the box straight into the path of the former England international, but Duffy was on the line to head it clear.
The sides remained deadlocked as the match headed into stoppage time, but Bolton had to finish the match a player short when Dorian Dervite was dismissed for a second bookable offence in the space of 10 minutes, bringing down Koita with a late challenge on the edge of the box, leaving the visitors to see out the final 30 seconds a player short.
The result moves Blackburn up to 20th in the table, while Bolton sit 22nd.