What's this sentence 麻烦包两份上次的礼盒 mean?
份(set/ suit/ ...) is a classifier for 礼盒 (gift box)
两份礼盒 = two sets of the gift box
麻烦 = to trouble (you) = Please
包 = pack
两份 = two sets of
上次的礼盒 = the gift box (I bought) last time

麻烦包两份上次的礼盒 = Please, pack me two sets of the gift box I bought last time

When you use 个 as the classifier for 礼盒, e.g. 两个礼盒, you are referring to the box itself
When you use 份 as the classifier for 礼盒, e.g. 两份礼盒, you are referring to all the items (the content) in the gift box, which need to be packed into one set

this sentence is about buying two packs of bouquets.

A bouquet is basically a collection of different flowers packed into one bundle or basket plus a card.
If you meant bouquet instead of gift box, you should write: &quot;Please, give me two of those bouquets I bought last time&quot;.
礼盒 (gift box) and 花束 (bouquet) are two different things.