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I can think of two reasons. One, they wanted to solidify the party members a bit, flesh out the relationship between Raphtalia and Filo so they're not just members of the same person's party, they're comrades themselves. Filo could've used a bit of fleshing out and it's good to occasionally take a break to just examine the relationships between characters and how they develop. That's part of the reason beach and hot spring episodes tend to happen I believe. Another big reason could be that they felt the plant monster wouldn't take a full episode, but the next major spot would require that or more. If this's the case, better to shove a half-ep filler in than to cut off at a bad point or rush an important scene to make it fit in the second half. Timing is important when you've got a specific number of minutes to fill up each week followed by a week-long wait for the next part; you can't just keep going and stop whenever. Just like adventurers sometimes have to stop at a village a few hours earlier than normal to avoid camping in a dangerous place, sometimes animators have to stop the main story early to avoid having to instead stop somewhere bad.
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