The NYT , in its front-page coverage, says the plane was flying far lower than the rules for training missions allow.
( ( The NYT ) ( , ( ( in ( its ( front-page coverage ) ) ) ( , ( ( says ( ( the plane ) ( was ( flying ( ( far lower ) ( than ( ( ( the rules ) ( for ( training missions ) ) ) allow ) ) ) ) ) ) ) . ) ) ) ) )
(ROOT (S (NP (DT The) (NNP NYT)) (, ,) (PP (IN in) (NP (PRP$ its) (JJ front-page) (NN coverage))) (, ,) (VP (VBZ says) (SBAR (S (NP (DT the) (NN plane)) (VP (VBD was) (VP (VBG flying) (ADVP (ADVP (RB far) (JJR lower)) (SBAR (IN than) (S (NP (NP (DT the) (NNS rules)) (PP (IN for) (NP (NN training) (NNS missions)))) (VP (VBP allow)))))))))) (. .)))
The NYT reported that training missions did allow for planes to fly that low. 
( ( The NYT ) ( ( reported ( that ( ( training missions ) ( did ( ( allow ( for planes ) ) ( to ( fly ( that low ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NNP NYT)) (VP (VBD reported) (SBAR (IN that) (S (NP (NN training) (NNS missions)) (VP (VBD did) (VP (VB allow) (PP (IN for) (NP (NNS planes))) (S (VP (TO to) (VP (VB fly) (S (NP (DT that)) (ADJP (JJ low))))))))))) (. .)))