Leaving them "unmarked" was probably somewhat underhanded - although avoidance of detection is a generally acceptable ruse of warfare. Plus no state of war existed then or now, so there can be no claims of violation of rules of warfare as stipulated by various international treaties. Just like when US had send undercover commando teams to Iraq prior to invasion.
As to sending our forces to Crimea per se - at that moment we had a right to hold a number of troops there (not restricted to naval personnel). Apparently the numbers actually there never exceeded the numbers allowed under treaties.
Nevertheless, I doubt that the presence of our troops had influenced the outcome of the referendum.