In this context, it means that the words appeared in a frequent but unplanned fashion during the conversation. It would also imply that there was something different about "these words", but I don't know without the context. For example, "their conversation was peppered with expletives" means that they swore frequently during their conversation. The swear words are the words that stand out from the other words in the conversation, in the same way that pepper stands out from the food that it was sprinkled on. Imagine grinding pepper over a meal. There are lots of bits of pepper all over the food, but they have landed randomly.