Hi !!
1- Shortly after the sun sets over the Pacific Crest Trail "come" the time of the day most favored by the deserts animals. => FALSE
Shortly after the sun sets over the Pacific Crest Trail comes the time of the day most favored by the desert animals. ► CORRECT
the subject "the time of the day" (singular) agrees with the verb "comes" = 3rd person singular, you must add an "s".
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2-Currently out of reach of human exploration, farther away from than our sun "lies" the planets Jupiter and Saturn. ==> FALSE
Currently out of reach of human exploration, farther away from our sun lie the planets Jupiter and Saturn. ► CORRECT
the subject "the planets" (plural ) agrees with the verb "lie" = no "s" at the 3rd person plural.
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3- The movie critique explained that there "were" an element of the plot that didn't make sense. ==> FALSE
The movie critique explained that there "was" an element of the plot that didn't make sense. ► CORRECT
there was an element => singular // there were many elements = plural
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Step-by-step explanation
The verbs take an "S" at the third person singular only at Present tense
there was + singular
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☺☺☺
there were + plural