Final answer:
The correct phrasal verb to fill in the blank is 'cropped up,' as it conveys the meaning of troubles appearing unexpectedly after a period of initial happiness.
Step-by-step explanation:
The correct phrasal verb to use in the sentence 'We were happy in the beginning, but now all troubles have A. cropped up. This phrase means that problems or difficulties have started to occur unexpectedly or have become apparent over time. 'Cropped up' best fits the context of troubles appearing after a period of happiness.
The other options, while related to occurrences and events, do not convey the same meaning of sudden or unexpected appearance as 'cropped up' does. For example, 'come about' typically means to happen, but without the connotation of being unexpected, 'come out' means to be revealed or become known, and 'rushed in' suggests a sudden and hasty arrival which does not necessarily equate to the gradual emergence of troubles.