Remove all perception of military usage of the word 'lieutenant' from your understanding of its usage here.

To start with the etymology, lieutenant is a combination of 'lieu', meaning instead, and 'tenant', meaning place or position. The word quite literally means 'person instead of'.

In the Royal (UK) Navy, 18th century, a ship would have the captain and his lieutenants (often ranked in order of first, second, third), the captain of marines and his officers. All of these held crown commissions. The lieutenants were subordinate only to the captain, in modern times we would call them the XO. Think Mr Spock or Commander Riker from Star Trek. All were all owners of commissions from the crown and likely sons of landed and titled gentry, if not gentry themselves. There was a similar practice of purchased commissions for officers in the army, especially in expensive cavalry units.

The system of purchased commissions phased out in the late 19th century. Most point to the Franco-Prussian War as the catalyst, as the French gentlemen-officers floundered against the profession of arms officers that received their promotions based off of merit, not simply seniority of title.

But it isn't just a military rank. It still means in lieu of. A lieutenant to someone is someone that person entrust with their command or authority in their absence. For example, lieutenant-governors serve just below the governor. Lord lieutenants are representatives of the sovereign in their county.

It is interesting how that usage is also in military ranks. While a major out ranks a lieutenant, a lieutenant-general (3 star) outranks a major-general (2 star). This is because lieutenant-general a modifier of the 4 star rank, which is simply general. Similarly, a lieutenant-colonel is just below a colonel.

Edit: off of mobile, I can expand some more in relation to your original question and add a source to back that up. Your question was what was Titus Labienus doing as one of Julius Caesar's lieutenants. Once again, we're using that word as a title or duty, not as a rank. Labienus was a legate. So was Caesar. So he was quite senior in the army, and led armies in Caesar's stead while on campaign with him, and later, led armies under Pompey against Caesar's 'revolutionaries'.

Sources: Francophone military officer, and I have previously been a lieutenant, but also https://www.history.navy.mil/research/library/online-reading-room/title-list-alphabetically/w/naval-traditions-names-of-rank/officer/lieutenant.html

Imperial Honorifics and Senatorial Status in Late Roman Legal Documents Mathisen, R. W., 2001, Law, Society, and Authority in Late Antiquity. Mathisen, R. W. (ed.). Oxford University Press, p. 179-207