The match at the Vasil Levski national stadium was interrupted for a few minutes midway through the first half after rival supporters threw fireworks at each other and a number of flares were hurled from the stands.
"I like such crowd that supports passionately and with heart, we're not in a library," Penev told reporters after Croatia's 1-0 win in the qualifying Group H match.
"There should be no punishment, we've had enough of these bans."
In March 2013, Bulgaria beat Malta 6-0 in a world qualifier played behind closed doors after their fans had been found guilty by FIFA of racist behaviour in a game against Denmark in October 2012.
The Bulgarian Football Union (BFU) were also fined 40,000 euros (31,410 pounds) by European football's governing body UEFA for racist abuse by fans in their Euro 2012 qualifier against England in September, 2011.
BFU president Borislav Mihaylov, who is also a UEFA executive committee member, said he would not be surprised if the governing body punished his team for the crowd disorder in the Croatia clash.
"Probably, we'll be punished," Mihaylov said after the match. "I do not know what will be our punishment."
Flares and fireworks are regularly seen at Bulgarian grounds and some supporters' groups want them to be allowed to use pyrotechnics in controlled conditions to enhance the atmosphere and fan choreography.
"These are our fans and I would like to thank them for their support," added Penev, a former Valencia, Atletico Madrid, Compostela and Celta Vigo striker.
"These are things that happen in the world. Smoke bombs, flares, the game was interrupted for five minutes and then we continue to play. Everything is okay."
(Editing by Nick Mulvenney)
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