“The Flea” uses enjambment irregularly, without a strong or regular pattern. The poem is more often end-stopped, which lends it a meditative feel, whereas the enjambments don't seem to follow a particularly strong rhyme or reason. For instance, the first stanza contains two enjambments, in lines 1 and 5, while the third stanza contains four, in lines 19, 21, 23, and 26. (We've noted line 1 as being enjambed because its full thought spills over onto line 2; despite the comma, you can't grasp the entire meaning of line 1 without the line that follows. The same is true of line 21, and perhaps also line 26.)
The irregularity of the enjambments makes them hard to predict—inserting moments of potential disruption into the speaker's otherwise plodding argument. Where the frequent end-stops make the speaker seem calm and collected—sure of his thoughts—the unpredictable enjambments may feel like cracks in his veneer, moments of him failing to maintain his nonchalance and rushing to convince his mistress of his argument. Note for example the particularly evocative enjambment of line 19: this is right after the mistress has killed the flea, and the speaker's words subsequently tumble out without regards to the line break, spilling over onto the next as the speaker rushes to convince the mistress that she's just sinned.
Of course, on a broader level, the lack of clear pattern in enjambment is not entirely surprising. Although each stanza of “The Flea” has an elaborate—and innovative—formal pattern, the poem is otherwise formally rather sloppy, full of strange and awkward metrical substitutions and arguably weak rhymes. Indeed, during his lifetime, Donne was famous for his carelessness in formal matters: the argument of his poems was more important to him than strict meter or, in this case, a strict pattern of enjambment.
It seems like the speaker uses enjambment when and where it is convenient for him to do so; he does not trouble himself much about building a consistent or clear pattern. This has some advantages for the speaker: it keeps the poem feeling fresh and conversational. Though the poem has an underlying—and highly significant—formal architecture, the speaker is not overbearing or pedantic in his commitment to that form: he lets the reader discover it for him or herself.