New Zealand's women's team said their training session on Monday had been disrupted by a drone flown by a staff member of their opening Group A opponents Canada.
Hubbard, 43, competed in men's weightlifting competitions before transitioning in 2013.
Save Women's Sport Australasia, a group opposed to transgender women competing in women's sports, said Hubbard's selection was allowed by "flawed policy from the IOC".
New Zealand Olympic Committee officials arrived in Delhi to inspect Commonwealth Games facilities and security after their team manager criticised the accommodation in place for athletes.
After days of indecision, the New Zealand Olympic Committee on Friday confirmed participation in the Delhi Commonwealth Games after seeing positive steps being taken by the organisers to improve the situation.
The Delhi Commonwealth Games organisers' failure to admit to problems with their preparations has seen them lose the faith of competing countries, New Zealand chef de mission Dave Currie said on Thursday.
New Zealand would not hesitate to withdraw from the Delhi Commonwealth Games if the country finds the security arrangements inadequate during its final assessment of the event's preparations in the next few days, according to media reports in Wellington.
The controversial Delhi Commonwealth Games is in the headlines again after sporting authorities in New Zealand claimed that they are owed a 'six-figure sum' by the event's organisers in India.
Saturday's blasts in Bangalore have triggered a security alarm for New Zealand's Olympic Committee, which is taking the incident seriously before finalising the contingent for the Delhi Commonwealth Games.
New Zealand's Olympic athletes and officials have been warned of the risk associated with the Zika virus on Friday, including the possibility that it could be sexually transmitted.
New Zealand hopes of becoming the first Olympic rugby sevens champions suffered a major setback on Tuesday when they lost their opening match to Japan and Sonny Bill Williams for the tournament to an Achilles injury.