Puel's side's disappointing showing against the 33-time Czech champions is a cause for concern for a variety of reasons. However, the Frenchman is remaining calm and upbeat amid a poor run of form.
Problems in front of goal
The trip to Sparta was arguably Southampton's biggest game of the season so far. After the historic victory over Inter Milan at St Mary's three weeks ago, the Saints knew that a victory in Prague would pretty much guarantee their place in the knockout stages of the Europa League.
However, it all went wrong. A well-worked, but atrociously defended, set-piece from the hosts was enough for them to get the victory they needed to ensure they will be playing European football after Christmas. In contrast, Puel's men now find their path to the last 32 far less straightforward.
Once again, the most notable facet of the game where Southampton were found wanting last night was creating and taking goal-scoring opportunities. The Saints have been unable to muster a single goal in their three European away games this season, despite having plenty of possession and chances in each of their trips around the continent.
However, it is not just on Thursday nights that the South Coast side have been struggling to find the net. As well as scoring only five times in the last eight games, Southampton have the worst shots-to-goal percentage (6.5%) in the Premier League. Whichever way you look at it, it seems they have a serious issue.
Despite the lack of creativity and cutting edge in his team, manager Puel has remained collected, describing last night's by saying "it's football and it's frustration". The Saints boss also focused on praising his players' efforts, maintaining that they created "good play, good possibility, good chances".
Similarly, Puel also denied any claims that Southampton did not show enough desire in the Czech capital, stating that "we have character" and "good spirit". He did however, accept the need to "find the clinical to finish our action".
While this positivity demonstrates Puel's belief in his players, Saints fans will be more worried about results improving on the pitch than the persistent optimism.
The poor showing in Prague last night means that Southampton face a winner-takes-all game at home to Hapoel Be'er-Sheva at St Mary's in a fortnight to decide who joins Sparta in the next round of the competition.
Once again, Puel's attitude was very much glass-half-full, focusing on how the game will be "fantastic for the fans", as the Saints have great chance to secure their qualification from a "very hard group".
If his side can get the win against the Israeli outfit in this season-defining game, then everyone on the South Coast will very much be buying into Puel's buoyant approach.