Ambiguity is probably a lack of intentional structure. Themes (like most story elements that exist outside the text in the reader's mind) need a beginning, middle, and end state to feel intentional.
The beginning establishes the status quo. It is the theme in its un-examined state, a naive or fairytale version. The theme in this state is so simple it can be expressed in just a few words: "love conquers all", "truth will out", "stay with your own kind". This version of the theme is presented as a universal fact (even if it isn't actually true).
The middle is where conflict or complication challenges this naive view. It takes the theme deeper, and makes it specific by applying it directly to characters and situations in the story. I've seen this called "the message" (probably because it is explicitly stated in the text, whereas the theme is not) but it's essentially the theme in a complicated state, with caveats and exceptions where the theme is no longer a "universal truth" – either the characters are fighting against it, or the plot is throwing try/fail cycles, or boy has lost girl. This might happen more than once and to different characters. The same naive theme, played out against multiple situations that seem to break or defy the theme.
In certain genres, thriller and horror for example, the theme-progression might be inverted. The simple version is the conclusion rather than the beginning, but it takes the whole story to break down the protagonist's resistance, or for the pieces to fall into place. A more complicated theme becomes simplified through reveals, or by removing the protagonist's options to escape the theme. (For example, a complicated real-world theme that says people are neither good or evil, evolves to "pure evil exists" as the other reasonable options are removed).
The end is of course the resolution(s) of the specific versions. Either the theme arrives back at its naive conclusion, or the narrative rejects the universal theme to emphasize the limits of the naive version.
If the naive theme is applied across various characters, and each conclusion is different, it might be interpreted as character failures – a parable usually explores a common theme with "good" and "bad" examples. Modern narratives tend to use character flaws to self-complicate, once protagonists stop resisting the theme is allowed to be "true". Antagonists are often "wrong" because they defy the theme (successfully, at least for a while) more than they directly confront the main characters.
You can structure a theme, the same as you can structure character or a romantic relationship, by plotting its development on a timeline. I don't agree that you should ignore themes entirely and they will subconsciously emerge in your writing – that is called subtext, which sure can be a theme but can also be unintentional. Themes should be intentional and reinforced by the narrative. They should be presented as in-world truths that evolve through states of reject/accept by the characters.