Pochettino's team were beaten 4-3 on penalties after being held to a goalless draw by a club 71 places below them, with Christian Eriksen and Lucas Moura both missing during the shoot-out.
It was appropriate that Eriksen's effort was saved as the Denmark playmaker has been focus for much of the unrest in the Tottenham camp.
Eriksen said he wanted a new challenge at the end of last season, but his hopes of securing a move were dashed.
Jan Vertonghen, Danny Rose, Toby Alderweireld and Victor Wanyama also endured uncertainty about their futures and, even now the transfer window is closed, it remains uncertain whether they have long-term prospects at the club.
Pochettino conceded there are still issues behind the scenes, contributing to Tottenham's lacklustre start just months after their incredible run to the Champions League final.
"When you have an unsettled squad always it's difficult and you lose time and then you need time to recover the time you lose," Pochettino told reporters.
"That's where we are. Maybe our performances are good but you need this extra, which is mental, connection, it's energy to be all together, not to have different agendas in the squad.
"We need time again to build that togetherness that you need when you are competing at this level.
"We are in a period where it's a bit tough for us but we keeping working to find a solution.
"When this type of thing happens it's about staying clear and fresh and calm. We're trying to find solutions and we only need time."