As Chelsea approach their Champions League reckoning against Nordsjaelland on Wednesday night, there are so many aspects of the club's current condition that might offer cause for concern: the supporters' attitude towards Rafa Benitez, the flat-lining form of Fernando Torres and the very real possibility that they could become the first defending champions of Europe eliminated in the group stages.

Yet as well as all these worries there is another cloud on the horizon that the club are uncertain how they can shift: a growing sense of gloom that the team are now reaping the effects of the bad will sown with referees over the Mark Clattenburg affair. It is a delicate situation, with no one at Chelsea suggesting that decisions are consciously being given against the club because of that episode with Clattenburg that ended in the Football Association deciding there was insufficient evidence to bring charges.

The club are also aware that every team has their complaints with officials, but the fear is that the current disconnect between the Chelsea team and the referees in charge of games is having a damaging effect on individual players. While paranoia about referees and the decisions of match officials is a common theme from the top to the bottom of the Premier League, it is indicative of how seriously Chelsea regard the situation with match officials that it is occupying minds at Stamford Bridge.

Just 13 days after the FA cleared Clattenburg, the club have adopted an unofficial policy of not criticising referees in post-match press conferences for fear of attracting allegations of bullying and intimidation when relations between them and the 16 Select Group officials are at their most fraught.

It was notable on Saturday that Benitez stopped short of saying anything that could have been construed as criticism of referee Martin Atkinson following the 3-1 defeat to West Ham. This was despite the reasonable expectation that he could have given a foul against Carlton Cole for the striker's challenge on Branislav Ivanovic for the Hammers' first goal.

Invited after the match to criticise Atkinson's decision to allow the goal to stand, Benitez simply said that it was "unlucky". There is a mood at the club that because of the allegations made against Clattenburg, and despite the FA's vindication of Chelsea's decision to make them, there is no scope to be seen as being critical. Although West Ham did have a Kevin Nolan goal disallowed for a shove by James Collins on Ivanovic, the club are concerned that communication between their players and officials on the pitch are becoming ever more fraught.

John Obi Mikel, at the centre of the Clattenburg allegations, was booked in the second half of Saturday's game for dissent. That was in spite of an atmosphere of robust exchanges between players on both sides and referee Atkinson during the match. Given the events of the last five weeks, Chelsea players feel that their ability to communicate with referees has been compromised.

Eden Hazard's recent run of poor form is a consequence, the club fear, of what they see as him earning an unwarranted reputation as a player who goes to ground too easily. His confidence is said to have been badly affected by a perceived lack of protection.

Despite their current situation, the club are preparing already for at least two new signings next month, with an appetite to go for Radamel Falcao if that is the player who they decide will make a critical difference to their season. The Atletico Madrid striker has a £41m buyout clause in his contract but that will not be regarded as an obstacle if signing him is identified as critical to the club's progress.

There are no current plans to bring Avram Grant on board as an adviser to Benitez, especially with the interim manager having such a clear idea of what his own playing style and approach will be. Nevertheless, Grant, most recently manager of Partizan Belgrade, remains very close to owner Roman Abramovich and, regardless of his track record as a coach, his influence can never be discounted.

As it stands, Benitez has the full backing of the board despite a start of just two points from his first three games in charge. The interim manager has been charged with giving the team a style and identity to match what the club and Abramovich regard as Chelsea's status within European football and the club believe there were signs in the first-half display against West Ham that they are making some progress.

In spite of the availability of Pep Guardiola this summer, and the increasingly fractious relations between Jose Mourinho and Real Madrid, Benitez has been told that if he makes a success of the Chelsea job then it will be his in the long term. The club are still convinced that they made the right decision in moving out Roberto Di Matteo when they did.

Chelsea face Nordsjaelland tomorrow and will only progress to the knockout stages if they win and Shakhtar Donetsk beat Juventus at home. It is not an inconceivable outcome even though Shakhtar are without the striker Luiz Adriano who was banned for one game for "violation of the principles of conduct" for scoring against Nordsjaelland two weeks ago when his side were trying to give the ball back to the Danish side.

That decision, it had been noted, was rushed through in reasonably quick time by Uefa's standards. As it stands, Chelsea have enough concerning them with their relationship with referees in the Premier League before extending those fears to the rest of Europe.

Refs' revenge: are chelsea paying the price?

* Chelsea's discipline in the Premier League after Mark Clattenburg's decisions in the 3-2 defeat against Manchester United on 28 October:

Fouls awarded against: 66

Fouls awarded for: 74

Yellow cards: 7 (1.16 per match)

Red cards: 0

* Decisions against Chelsea since the Clattenburg incident:

11 Nov Chelsea 1-1 Liverpool

Luis Suarez appeared to push Ramires, who had been holding his shirt, before heading in from the corner to equalise.

17 Nov WBA 2-1 Chelsea

Chelsea denied a penalty for Claudio Yacob's apparent shove on Victor Moses, plus Eden Hazard's shot appeared to hit the arm of Jonas Olsson in the area – nothing was given.

1 Dec West Ham 3-1 Chelsea

Carlton Cole looked to have jumped unfairly with Branislav Ivanovic to equalise with a header.