The former Crystal Palace winger started the first group game against Iran but struggled to replicate his pre-tournament form and was subsequently substituted in the game in what looked like a precautionary move by team officials.
He did not make the bench against Bosnia-Herzegovina. which raised a lot of questions but he later took to the social media micro-blogging site, Twitter, to explain that he had a slight niggle and would be fit for the last group game against South American giants, Argentina.
Michael Babatunde started the Bosnia-Herzegovina game, and was later replaced by Ejike Uzoenyi as the Super Eagles won the game 1-0 in the second Group F game on 21 June.
Matters came to a head when Stephen Keshi later revealed to journalists that he was unaware of the player's injury concerns.
"I'm not aware that Moses has any injury problem," he said when asked about the fitness of the player, who has not featured for Nigeria since the opening day draw with Iran.
Moses was subsequently missing from the last Group F game with Argentina to fuel speculation that something was amiss, as he did not join the pre-match warm-up although Fifa had earlier listed him injured in their match day programme.
The 'Big Boss' was however quick to douse any fire insisting that there is nothing wrong between him and Moses as the Eagles were a united front.
"It's a purely medical issue. My last child is older than Moses, so why will I quarrel with my son?" Keshi
"People must find out facts and not speculate especially when they have a capable media person in our midst."
A source close to the team's camp told supersport.com that Moses needs to imbibe team spirit as his demeanor has not been good lately.
"Moses is a young lad, but he needs to understand the concept of team bonding and unity. His attitude has to improve.
"Some of the federation members here are also not happy with him, I think he can do better because he is a good footballer. He just needs to improve his attitude," the team source said.
Nigeria came second behind Argentina in Group F of the 2014 Fifa World Cup and will face France in the second round on 30 June in Brasilia.