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It’s one of those words. I hear it mispronounced almost as often as it is pronounced correctly. The curious thing about it is that it really only has two parts, both of which are simple word-sounds in their own right: new and clear. I even hear people who work closely with things nu-cue-ler get it wrong.
There’s a theory that the British, and a few others, pronounce the word lieutenant as LEFtenant because the French “lieu” at the start was originally “luef”. However, I suspect that actually there came a point when the majority pronounced it incorrectly and it became the accepted British pronunciation.
Maybe new-clear will eventually be forgotten in favour of new-queue-lar.

Pronunciation is a curious thing. I expect the list is very long and finds a home amongst both the well-heeled and the down-at-heel. So we have Magdalen College Oxford which we are admonished to pronounce in the medieval way “Maudlin”. This pronunciation evolved over time, but at least the middle-English speakers had the sense to spell it “Maudlyn”.
Incidentally, I’m over my irritation at nu-cue-ler (until next time). People should pronounce as they see fit, providing they are understood.
As for lieutenant, I imagine that originally the officer would be “the General’s” lieutenant and so on, i.e. a specific officer’s deputy and that over time it was formalised as a rank. The British Army still has Lieutenant General and Lieutenant Colonel in addition to Lieutenant and Second Lieutenant.

Perhaps it’s the same. Place holder for the captain under whose command the lieutenant is acting. Does that make sense?
Re pronunciation, here’s the OED:

The origin of the βtype of forms (which survives in the usual British pronunciation, though the spelling represents the αtype) is difficult to explain. The hypothesis of a mere misinterpretation of the graphic form (u read as v), at first sight plausible, does not accord with the facts. In view of the rare Old French form luef for lieu (with which compare especially the 15th cent. Scots forms luf-, lufftenand above) it seems likely that the labial glide at the end of Old French lieu as the first element of a compound was sometimes apprehended by English-speakers as a v or f. Possibly some of the forms may be due to association with leave n.1 or lief adj.

In 1793 Walker gives the actual pronunciations as /lɛv-/ /lɪvˈtɛnənt/ , but expresses the hope that ‘the regular sound, lewtenant’ will in time become current. In England this pronunciation /ljuːˈtɛnənt/ is almost unknown. A newspaper quot. of 1893 in Funk’s Standard Dict. Eng. Lang. says that /lɛfˈtɛnənt/ is in the U.S. ‘almost confined to the retired list of the navy’.