。
She must have been feeling unwell.
Literal
She [topic-は] condition [subject-が] was-bad must-be.
~に違いない expresses strong inference — 'must be the case that X / no doubt X' — based on observed evidence. Polite form: ~に違いありません. It's stronger than ~だろう ('probably') and more confident than ~と思う ('I think'). 具合が悪い is the standard health idiom: 具合 ('condition, state') as the が-marked subject and 悪い ('bad') as the predicate, the whole expression meaning 'feeling unwell.' Note the past tense was-bad, with present-tense 違いない — Japanese keeps the inference tense neutral while the inferred state takes its own past form.