Fareham suffered Hampshire Cup heartache after Trojans beat them in the semi-final on Saturday.
The National League conference west side began the day well with a comprehensive 7-1 victory over Basingstoke in the quarter-finals.
But in their second game of the day, they drew 1-1 with Trojans before going down 3-1 on penalties.
Performance director Ben Barnes thought his side were at a disadvantage by having to play two matches in one day, while their opponents only had one after Hamble pulled out at the last minute.
‘It was an ultimately disappointing end to the campaign,’ said Barnes.
‘Last season we had a bye to the semi-final as Bournemouth pulled out and we were the fresher team against Southampton University, who had played in the morning.
‘But this year we are a victim of the system as Trojans were fresher and we struggled to break them down.
‘It needs to be looked into because there is a free weekend before the cup final but we had to play two games in one day.
‘That is fine if everyone played two matches but clearly that does not happen as teams have pulled out before the day for the second year in a row.’
Fareham comfortably saw off Basingstoke in their opening match.
Ben Hibberd scored a hat-trick, while Josh Godfrey added two goals.
Jamie Young netted on his first-team debut and James Seager completed the scoring.
‘It was a comfortable win in the end against Basingstoke, even though we made hard work of it in the first half,’ added Barnes.
The Henry Cort side started well in their semi-final clash with Trojans and went 1-0 up through a penalty corner rebound scored by Jon Potts.
However, the Southampton side equalised and then went on to win 3-1 on penalties.
Barnes added: ‘With the game going straight to penalties, with no extra-time after the very short 25 minutes each-way game, we were left with the lottery of penalty strokes.
Trojans took theirs better than we did, simple as that.’