Here are premises. First, both words are not of everyday-use but the words used by people in the field. Next, you can easily figure out while 物流 is a general Japanese word, ロジスティクス is the word coming from English. Most of Japanese know the first, but few can make out what it exactly means. Then, the usages of the words. These two, in the most of the cases, are used as adjectives to modify nouns, and the nouns decide which you use. When the noun is an English-rooted word like オペレーター, ロジスティクス fits in well. And when the noun is a general Japanese word like 業者, 物流 is the one you should use.