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The cuttlefish which the Radzyners use only turns blue with the aid of chemicals (pottassium and iron) which Rav Herzog found would turn any organic compound that color. So the cuttlefish dye had nothing to do with the turning blue which is a problem.
One problem with the murex trunculus is that it is chemically identical to kala ilan. The gemara gives chemical tests that can distinguish between real techeiles and kala ilan. Now if they were chemically identical then no test would be able to distinguish between them. Another problem is that it doesn’t really fit into most of the Gemara’s descriptions of the chilazon (comes up once in 70 years, domeh layam, the dye is better while it’s alive, etc.) unless you deviate from the standard pshat.