At least one of the problems is that you don't zero-initialize your child array.

class Active { //SuffixTree::Active
	public:
		int edge,length;
		SuffixNode* node;
		Active() : node(nullptr),edge(-1),length(0) {}
};

• In constructor 'SuffixTree::Active::Active()':
• main.cpp|46|warning: 'SuffixTree::Active::node' will be initialized after [-Wreorder]|``
• main.cpp|45|warning: 'int SuffixTree::Active::edge' [-Wreorder]|
• main.cpp|47|warning: when initialized here [-Wreorder]|

I think it might be this way:

class Active {
	public:
                SuffixNode* node;
		int edge,length;
		Active() : node(nullptr),edge(-1),length(0) {}
};

root->child[Input(i)] = new SuffixNode(i,&end);

• main.cpp||In member function 'void SuffixTree::build()':|
• main.cpp|74|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp|82|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp|105|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp|106|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp|108|warning: array subscript has type 'char' [-Wchar-subscripts]|

SuffixNode* selectNode(int i) {
	return active.node->child[Input(i)];
}

• main.cpp||In member function 'SuffixTree::SuffixNode* SuffixTree::selectNode(int)':|
• main.cpp|123|warning: array subscript has type 'char' [-Wchar-subscripts]|

All other warnings are about using chars as SuffixNode ans vice versa

• main.cpp||In member function 'char SuffixTree::nextChar(int)':|
• main.cpp|130|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp|132|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp||In member function 'void SuffixTree::walkDown(int)':|
• main.cpp|149|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp||In function 'void recc(SuffixTree::SuffixNode*, int, int, Sol*)':|
• main.cpp|184|warning: array subscript has type 'char' [-Wchar-subscripts]|
• main.cpp||In function 'int main()':|
• main.cpp|201|warning: array subscript has type 'char' [-Wchar-subscripts]|

Hope it help :3

Debugger also said that program crashes on line 70

active.edge = selectNode(i)->start;

You should check it when global var SuffixTree tree initialized