Lion fish never grow as large as shown. A lot of the fish look bigger than they really are when looking out the window of the submarine.
After the becalmed ship Amelie is sunk by the submarine, its sails continue to hang from their spars instead of floating around. Although linen sails are heavier than water, by the late 1890s these had been replaced by cotton, which is lighter.
This movie is obviously set in the late 19th century - the 1890s. The steamship Savannah in the opening of the film crossed the Atlantic in 1819 - a good 70 years before the story takes place.
There are a few single frames in the original release that have Karel Zeman posing his work. Several are during the small sub rescue in the underwater cave. The original American release still has these mistakes. The remastered versions have these taken out. These can still be seen in the bonus featurette that is included with the remastered Blu-ray Disc release.