The 1991 referendum was definitely an independence referendum. As the Wikipedia article on it says:
The referendum did not just call for the restoration for the ASSR, but
further called for Crimea to be a participant in the New Union Treaty
– an ultimately futile attempt by Mikhail Gorbachev to reconstitute
the USSR. This would have meant that Crimea would have been a
sovereign subject of the renewed USSR[10] and separate from the
Ukrainian SSR (emphasis mine).
Crimeans plans were to establish themselves as an independent, sovereign state, and they chosed the path of least resistance they saw: becoming an ASSR, joining the New Union Treaty and establish their independence. The fall of the Soviet Union before the New Union Treaty could materialize left them in a limbo, caught in the step 1 of the process - becoming an ASSR - without a way to make it into step 2.
With the fall of the Soviet Union later that year, Ukraine accepted Crimea's new name, but not its status. So is, Crimea could call itself "autonomous", but it wasn't. Ukraine called a referendum to declare itself independent, but approval was low in Crimea. In May 1992, Crimea's parliament then declared independence from Ukraine, but Kiev's authority called that decision illegal. Again, Crimea's parliament decided to postpone the referendum that should ratificate the decision - but they didn't cancelled it.
In 1994, they run again another referendum of independence, and this time they went ahead despite Ukraine's wishes - Ukraine was suffering the economic collapse of all ex-soviet republics, and had been stripped of its nuclear weapons, so they probably thought they couldn't afford a military operation. The 1994 referendum asked for Crimeans to have dual ukrainian/russian citizenship, President of Crimea's decrees having status of law and relationship between Crimea and Ukraine to be defined in a Treaty - so is, de facto independence, even if Ukraine wanted to keep considering Crimea as part of Ukraine. The three questions were aproved by solid majorities - even if the USSR didn't exist anymore.
The situation deteriorated rapidly, with Crimean authorities creating state agencies and infrastructures as if they were actually sovereign, until Ukraine sent the army in.
The situation became so threatening that the Ukrainian authorities
were forced to take decisive measures to restore Ukrainian sovereignty
on the peninsula. In March 1995, the Ukrainian Parliament abolished
the Crimean Constitution and the office of the President of Crimea.
Soldiers of the National Guard of Ukraine and Ukrainian special forces
were transferred to the peninsula.
All in all, Crimea staying in Ukraine despite wanting to be independent is not different from Ukraine voting that ukrainian laws have precedence over soviet laws, but not outright declaring independence back in 1990. Declaring independence of a part of the country is usually met by a military response from the central government - it's not just that a powerful USRR would sent its tanks to Prague, it's that UK sent its army against Washington, and Lincoln sent the Union Army against the Confederates. When you're dealing with independence, cautious steps are sensible options. Ukraine only declared itself independent after the definitive collapse of the USSR, while Crimea's attempts of independence in 1991 and 1994 were ignored or crushed, and only the one in 2014 - with russian troops on the territory - went ahead.