yes, second "ise" is not needed here. You can write it as -
इसे ब्रिटेन के समय के मुताबिक़ दो बजे दोपहर में मैनचेस्टर में उतरना था |
and yes , "ise" here is refering to the plane.
" According to the UK it was expected to arrive in Manchester at two o'clock in the afternoon."
"ise" means "it".