The 43-year-old former Ton, Chelsea, Crystal Palace, Leeds United, and Bradford City midfielder was absent from the dugout for Saturday’s win over Dundee.
Sources have suggested that he and manager Kenny Shiels do not see eye to eye and that Hopkin, who took up the role as assistant last December, elected to stay away at the weekend.
When contacted by the Tele, the Northern Irishman declined to comment on Hopkin’s whereabouts on Saturday but insisted that there had been no fall-out between the pair.
Greenock-born Hopkin both began and finished his playing career with his local club and had a brief spell as caretaker manager alongside Derek Collins following his retirement in 2002.
He returned to Cappielow a decade later in a coaching capacity when consultant for club development Warren Hawke installed him as reserve team boss.
The former Scotland internationalist impressed and was given further responsibilities upon the establishment of a full-time development squad last summer.
Part of his remit is to work with a group of the club’s youth academy graduates on a daily basis as well as managing the reserves on a match day.
Since taking sole control of the second string in August 2012, Hopkin has guided them to second and third place finishes in the reserve league.
As well as taking them to the Reserve League cup semi-final stage this term, he was also in charge of the Under-20s side which reached the Scottish Youth Cup quarter-finals.
It remains unclear whether or not Hopkin will remain in charge of the development squad, and neither he nor anyone from the club was available for comment.