Arriva Trains Wales said the matter was an issue for Network Rail and its contractor.
The Mountsorrel quarry donated ballast and the charity bought second-hand track from Network Rail.
Transport Secretary Stewart Stevenson said Network Rail had briefed him on the events at Halkirk.
Network Rail said the surest way to prevent any accidents was to close level crossings.
BBC: Level crossings: Wales safety work after 33 near misses
Railway cable theft in Yorkshire has fallen heavily, according to figures from Network Rail.
However, Network Rail said the recent severe weather had prevented the completion of three new stations.
Scotland's Network Rail director Ron McAulay said the stations would be completed once the weather improved.
"Decisions on bonuses are a matter for Network Rail's independent Remuneration Committee, " he added.
Essential maintenance work to Selby's swing bridge had been planned two years ago, Network Rail said.
Last year, Network Rail released footage in Llanelli to highlight the potential dangers of level crossings.
Network Rail will provide a new car park at Irvine station and increased parking at Bathgate.
Network Rail said it was working with archaeologists to uncover and record the roundhouses.
Industrial partners on the project include Sellafield, the National Nuclear Laboratory, BAE Systems and Network Rail.
However, the plans will be affordable only if Network Rail manages to make these savings.
Network Rail said it wanted to stress the increased dangers of trespassing on the tracks.
The crossing will remain closed for a further six months, Network Rail spokesman Martin Frobisher said.
BBC: Moor Bridge footbridge project criticised by Sherwood MP
Network Rail hopes to cram in 20 weekends' worth of work in the period.
BBC: Reading station delays warning as upgrade works ramped up
Steve Montgomery from First ScotRail and Ron McAulay and David Simpson from Network Rail.
The station in Whitby is owned by Network Rail and run by Northern Rail.
BBC: Whitby businesses and railway share ?3.4m seaside grant
Network Rail said services to London Waterloo were not due to restart until Monday.
Network Rail officially took over responsibility for delivering the new route from Transport Scotland last month.
Network Rail said all four lines were open, with three lines open to electric trains.
In the newly-published report, Network Rail is criticised over the safety of the crossing.
Lines between Maidenhead and Slough were affected due to Network Rail signalling problems earlier.
BBC: Signal failure delays commuters travelling west of London
Network Rail said the driver noticed the gap as he passed it on an adjacent track.
Network Rail has advised passengers to check National Rail Enquiries for the latest information.
In the year 2002-03, including six months when Network Rail was in charge, punctuality averaged 79.2%.
Network Rail said the network and services in the east of England were set to grow.
BBC: Hopes for new stations but campaign wants faster trains
Network Rail said it needed to invest now to create a more resilient railway.
Details of where and when the public exhibitions will be held are on Network Rail's website.
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